------------------------------- command_history_12-04-2013.txt -------------------------------- 781 MMPBSA.py --help 796 nohup MMPBSA.py -O -i 4FVT_v1_mmpbsa_t01.in -o 4FVT_v1_mmpbsa_t01_06md.dat -sp 4FVT_v1.prmtop -cp 4FVT_v1_tern.prmtop -rp 4FVT_v1_SIRT3_AceCS2_rec2.prmtop -lp 4FVT_v1_NADp_lig2.prmtop -y 4FVT_v1_SIRT3_06md.dcd >& 4FVT_v1_mmpbsa_t01.log & 1037 nohup MMPBSA.py -O -i 4FVT_v1_fixed2_mmpbsa_t01.in -o 4FVT_v1_fixed2_mmpbsa_t01_03md.dat -sp 4FVT_v1_fixed2.prmtop -cp 4FVT_v1a_tern.prmtop -rp 4FVT_v1a_SIRT3_AceCS2_rec2.prmtop -lp 4FVT_v1a_NADp_lig2.prmtop -y 4FVT_v1_fixed2_03md.dcd >& 4FVT_v1_fixed2_mmpbsa_t01.log & 528 ./remove_duplicate.pl 4BVH_AADRP_h2l_small-4-7a_XP124_mmgbsa-out.txt > 4BVH_AADRP_h2l_small-4-7a_XP124_mmgbsa-out_unique.txt 529 ./merge_hits.pl 4BVG_Int_h2l_small_4-7a-XP100_mmgbsa-out_unique.txt 4BVG_enz_h2l_small_4-7a_XP110_mmgbsa-out_unique.txt 4BVH_AADRP_h2l_small-4-7a_XP124_mmgbsa-out_unique.txt > 4BVG_Int_enz_4BVH_AADRP_h2l_small-4-7a_mmgbsa-out_merged.txt 531 vi ./merge_hits.pl 582 perl Ante_RED-1.5.pl NAM_1.pdb > j1_ante_RED.log 599 cat RED-vIII.52.pl 600 m RED-vIII.52.pl 610 tail RED-vIII.5.pl 614 vi RED-vIII.52.pl 617 perl RED-vIII.52.pl >& j1_RED.log & 722 ./remove_duplicate.pl 4BVH_AADRP_h2l_small-8-12abc_XP123_mmgbsa-out.txt > 4BVH_AADRP_h2l_small-8-12abc_XP123_mmgbsa-out_unique.txt 723 ./merge_hits.pl 4BVG_Int_h2l_small_8-12abc-XP103_mmgbsa-out_unique.txt 4BVG_enz_h2l_small_8-12abc_XP127_mmgbsa-out_unique.txt 4BVH_AADRP_h2l_small-8-12abc_XP123_mmgbsa-out_unique.txt > 4BVG_Int_enz_4BVH_AADRP_h2l_small-8-12abc_mmgbsa-out_merged.txt 955 cat merge_hits.pl 959 vi merge_hits.pl 962 ./merge_hits.pl 4BVG_Int_h2l_smal02-17-prime_mmgbsa-out_unique.txt 4BVG_enz_h2l_small_02-17-XP99_mmgbsa-out_unique.txt 4BVH_AADRP_h2l_small-2-17_XP122_mmgbsa-out_unique.txt > 4BVG_Int_enz_4BVH_AADRP_h2l_small_2-17_mmgbsa-out_merged_v2.txt 966 ./merge_hits.pl 4BVG_Int_h2l_small_20-24-XP104_mmgbsa-out_unique.txt 4BVG_enz_h2l_small_20-24-XP112_mmgbsa-out_unique.txt 4BVH_AADRP_h2l_small_20-24-XP114_mmgbsa-out_unique.txt > 4BVG_Int_enz_4BVH_AADRP_h2l_small_20-24_mmgbsa-out_merged_v2.txt 968 ./merge_hits.pl 4BVG_Int_h2l_small_4-7a-XP100_mmgbsa-out_unique.txt 4BVG_enz_h2l_small_4-7a_XP110_mmgbsa-out_unique.txt 4BVH_AADRP_h2l_small-4-7a_XP124_mmgbsa-out_unique.txt > 4BVG_Int_enz_4BVH_AADRP_h2l_small-4-7a_mmgbsa-out_merged_v2.txt 970 ./merge_hits.pl 4BVG_Int_h2l_small_8-12abc-XP103_mmgbsa-out_unique.txt 4BVG_enz_h2l_small_8-12abc_XP127_mmgbsa-out_unique.txt 4BVH_AADRP_h2l_small-8-12abc_XP123_mmgbsa-out_unique.txt > 4BVG_Int_enz_4BVH_AADRP_h2l_small-8-12abc_mmgbsa-out_merged_v2.txt 972 ./merge_hits.pl 4BVG_Int_h2l_small_acid-XP105_mmgbsa-out_unique.txt 4BVG_enz_h2l_small_acid-XP113_mmgbsa-out_unique.txt 4BVH_AADRP_h2l_small-acids_XP125_mmgbsa-out_unique.txt > 4BVG_Int_enz_4BVH_AADRP_h2l_small_small-acids_mmgbsa-out_merged_v2.txt 976 cp ./merge_hits.pl merge_hits_v2.pl 977 vi merge_hits_v2.pl 979 ./merge_hits_v2.pl 4BVG_Int_h2l_small_acid-XP105_mmgbsa-out_unique.txt 4BVG_enz_h2l_small_acid-XP113_mmgbsa-out_unique.txt 4BVH_AADRP_h2l_small-acids_XP125_mmgbsa-out_unique.txt > 4BVG_Int_enz_4BVH_AADRP_h2l_small_small-acids_mmgbsa-out_merged_v2.txt 980 ./merge_hits_v2.pl 4BVG_Int_h2l_small_8-12abc-XP103_mmgbsa-out_unique.txt 4BVG_enz_h2l_small_8-12abc_XP127_mmgbsa-out_unique.txt 4BVH_AADRP_h2l_small-8-12abc_XP123_mmgbsa-out_unique.txt > 4BVG_Int_enz_4BVH_AADRP_h2l_small-8-12abc_mmgbsa-out_merged_v2.txt 981 ./merge_hits_v2.pl 4BVG_Int_h2l_small_4-7a-XP100_mmgbsa-out_unique.txt 4BVG_enz_h2l_small_4-7a_XP110_mmgbsa-out_unique.txt 4BVH_AADRP_h2l_small-4-7a_XP124_mmgbsa-out_unique.txt > 4BVG_Int_enz_4BVH_AADRP_h2l_small-4-7a_mmgbsa-out_merged_v2.txt 982 ./merge_hits_v2.pl 4BVG_Int_h2l_small_20-24-XP104_mmgbsa-out_unique.txt 4BVG_enz_h2l_small_20-24-XP112_mmgbsa-out_unique.txt 4BVH_AADRP_h2l_small_20-24-XP114_mmgbsa-out_unique.txt > 4BVG_Int_enz_4BVH_AADRP_h2l_small_20-24_mmgbsa-out_merged_v2.txt 983 ./merge_hits_v2.pl 4BVG_Int_h2l_smal02-17-prime_mmgbsa-out_unique.txt 4BVG_enz_h2l_small_02-17-XP99_mmgbsa-out_unique.txt 4BVH_AADRP_h2l_small-2-17_XP122_mmgbsa-out_unique.txt > 4BVG_Int_enz_4BVH_AADRP_h2l_small_2-17_mmgbsa-out_merged_v2.txt --------------------------------------------- command_history_11-27.txt -------------------------------------------- 794 MMPBSA.py --help 796 nohup MMPBSA.py -O -i 4FVT_v1_mmpbsa_t01.in -o 4FVT_v1_mmpbsa_t01_06md.dat -sp 4FVT_v1.prmtop -cp 4FVT_v1_tern.prmtop -rp 4FVT_v1_SIRT3_AceCS2_rec2.prmtop -lp 4FVT_v1_NADp_lig2.prmtop -y 4FVT_v1_SIRT3_06md.dcd >& 4FVT_v1_mmpbsa_t01.log & 389 ./remove_duplicate.pl 4BVH_AADRP_h2l_small-2-17_XP122_mmgbsa-out.txt > 4BVH_AADRP_h2l_small-2-17_XP122_mmgbsa-out_unique.txt 390 ./remove_duplicate.pl 4BVG_enz_h2l_small_4-7a_XP110_mmgbsa-out.txt > 4BVG_enz_h2l_small_4-7a_XP110_mmgbsa-out_unique.txt 391 ./remove_duplicate.pl 4BVG_enz_h2l_small_8-12abc_XP127_mmgbsa-out.txt > 4BVG_enz_h2l_small_8-12abc_XP127_mmgbsa-out_unique.txt 392 ./merge_hits.pl 4BVG_Int_h2l_small_4-7a-XP100_mmgbsa-out_unique.txt 4BVG_enz_h2l_small_4-7a_XP110_mmgbsa-out_unique.txt 393 ./merge_hits.pl 4BVG_Int_h2l_small_4-7a-XP100_mmgbsa-out_unique.txt 4BVG_enz_h2l_small_4-7a_XP110_mmgbsa-out_unique.txt > 4BVG_Int_enz_h2l_small_4-7a_mmgbsa-out_merged.txt 395 ./merge_hits.pl 4BVG_Int_h2l_small_8-12abc-XP103_mmgbsa-out_unique.txt 4BVG_enz_h2l_small_8-12abc_XP127_mmgbsa-out_unique.txt > 4BVG_Int_enz_h2l_small_8-12abc_mmgbsa-out_merged.txt 396 ./merge_hits.pl 4BVG_Int_h2l_smal02-17-prime_mmgbsa-out_unique.txt 4BVG_enz_h2l_small_02-17-XP99_mmgbsa-out_unique.txt 4BVH_AADRP_h2l_small-2-17_XP122_mmgbsa-out_unique.txt > 4BVG_Int_enz_4BVH_AADRP_h2l_small_2-17_mmgbsa-out_merged.txt 473 ./remove_duplicate.pl 4BVH_AADRP_h2l_small-acids_XP125_mmgbsa-out.txt > 4BVH_AADRP_h2l_small-acids_XP125_mmgbsa-out_unique.txt 475 ./merge_hits.pl 4BVG_Int_h2l_small_acid-XP105_mmgbsa-out_unique.txt 4BVG_enz_h2l_small_acid-XP113_mmgbsa-out_unique.txt 4BVH_AADRP_h2l_small-acids_XP125_mmgbsa-out_unique.txt > 4BVG_Int_enz_4BVH_AADRP_h2l_small_small-acids_mmgbsa-out_merged.txt 528 ./remove_duplicate.pl 4BVH_AADRP_h2l_small-4-7a_XP124_mmgbsa-out.txt > 4BVH_AADRP_h2l_small-4-7a_XP124_mmgbsa-out_unique.txt 529 ./merge_hits.pl 4BVG_Int_h2l_small_4-7a-XP100_mmgbsa-out_unique.txt 4BVG_enz_h2l_small_4-7a_XP110_mmgbsa-out_unique.txt 4BVH_AADRP_h2l_small-4-7a_XP124_mmgbsa-out_unique.txt > 4BVG_Int_enz_4BVH_AADRP_h2l_small-4-7a_mmgbsa-out_merged.txt 531 vi ./merge_hits.pl 582 perl Ante_RED-1.5.pl NAM_1.pdb > j1_ante_RED.log 599 cat RED-vIII.52.pl 600 m RED-vIII.52.pl 610 tail RED-vIII.5.pl 614 vi RED-vIII.52.pl 617 perl RED-vIII.52.pl >& j1_RED.log & 722 ./remove_duplicate.pl 4BVH_AADRP_h2l_small-8-12abc_XP123_mmgbsa-out.txt > 4BVH_AADRP_h2l_small-8-12abc_XP123_mmgbsa-out_unique.txt 723 ./merge_hits.pl 4BVG_Int_h2l_small_8-12abc-XP103_mmgbsa-out_unique.txt 4BVG_enz_h2l_small_8-12abc_XP127_mmgbsa-out_unique.txt 4BVH_AADRP_h2l_small-8-12abc_XP123_mmgbsa-out_unique.txt > 4BVG_Int_enz_4BVH_AADRP_h2l_small-8-12abc_mmgbsa-out_merged.txt 958 cat merge_hits.pl 961 vi merge_hits.pl 962 ./merge_hits.pl 4BVG_Int_h2l_smal02-17-prime_mmgbsa-out_unique.txt 4BVG_enz_h2l_small_02-17-XP99_mmgbsa-out_unique.txt 4BVH_AADRP_h2l_small-2-17_XP122_mmgbsa-out_unique.txt > 4BVG_Int_enz_4BVH_AADRP_h2l_small_2-17_mmgbsa-out_merged_v2.txt 966 ./merge_hits.pl 4BVG_Int_h2l_small_20-24-XP104_mmgbsa-out_unique.txt 4BVG_enz_h2l_small_20-24-XP112_mmgbsa-out_unique.txt 4BVH_AADRP_h2l_small_20-24-XP114_mmgbsa-out_unique.txt > 4BVG_Int_enz_4BVH_AADRP_h2l_small_20-24_mmgbsa-out_merged_v2.txt 968 ./merge_hits.pl 4BVG_Int_h2l_small_4-7a-XP100_mmgbsa-out_unique.txt 4BVG_enz_h2l_small_4-7a_XP110_mmgbsa-out_unique.txt 4BVH_AADRP_h2l_small-4-7a_XP124_mmgbsa-out_unique.txt > 4BVG_Int_enz_4BVH_AADRP_h2l_small-4-7a_mmgbsa-out_merged_v2.txt 970 ./merge_hits.pl 4BVG_Int_h2l_small_8-12abc-XP103_mmgbsa-out_unique.txt 4BVG_enz_h2l_small_8-12abc_XP127_mmgbsa-out_unique.txt 4BVH_AADRP_h2l_small-8-12abc_XP123_mmgbsa-out_unique.txt > 4BVG_Int_enz_4BVH_AADRP_h2l_small-8-12abc_mmgbsa-out_merged_v2.txt 972 ./merge_hits.pl 4BVG_Int_h2l_small_acid-XP105_mmgbsa-out_unique.txt 4BVG_enz_h2l_small_acid-XP113_mmgbsa-out_unique.txt 4BVH_AADRP_h2l_small-acids_XP125_mmgbsa-out_unique.txt > 4BVG_Int_enz_4BVH_AADRP_h2l_small_small-acids_mmgbsa-out_merged_v2.txt 976 cp ./merge_hits.pl merge_hits_v2.pl 977 vi merge_hits_v2.pl 979 ./merge_hits_v2.pl 4BVG_Int_h2l_small_acid-XP105_mmgbsa-out_unique.txt 4BVG_enz_h2l_small_acid-XP113_mmgbsa-out_unique.txt 4BVH_AADRP_h2l_small-acids_XP125_mmgbsa-out_unique.txt > 4BVG_Int_enz_4BVH_AADRP_h2l_small_small-acids_mmgbsa-out_merged_v2.txt 980 ./merge_hits_v2.pl 4BVG_Int_h2l_small_8-12abc-XP103_mmgbsa-out_unique.txt 4BVG_enz_h2l_small_8-12abc_XP127_mmgbsa-out_unique.txt 4BVH_AADRP_h2l_small-8-12abc_XP123_mmgbsa-out_unique.txt > 4BVG_Int_enz_4BVH_AADRP_h2l_small-8-12abc_mmgbsa-out_merged_v2.txt 981 ./merge_hits_v2.pl 4BVG_Int_h2l_small_4-7a-XP100_mmgbsa-out_unique.txt 4BVG_enz_h2l_small_4-7a_XP110_mmgbsa-out_unique.txt 4BVH_AADRP_h2l_small-4-7a_XP124_mmgbsa-out_unique.txt > 4BVG_Int_enz_4BVH_AADRP_h2l_small-4-7a_mmgbsa-out_merged_v2.txt 982 ./merge_hits_v2.pl 4BVG_Int_h2l_small_20-24-XP104_mmgbsa-out_unique.txt 4BVG_enz_h2l_small_20-24-XP112_mmgbsa-out_unique.txt 4BVH_AADRP_h2l_small_20-24-XP114_mmgbsa-out_unique.txt > 4BVG_Int_enz_4BVH_AADRP_h2l_small_20-24_mmgbsa-out_merged_v2.txt 983 ./merge_hits_v2.pl 4BVG_Int_h2l_smal02-17-prime_mmgbsa-out_unique.txt 4BVG_enz_h2l_small_02-17-XP99_mmgbsa-out_unique.txt 4BVH_AADRP_h2l_small-2-17_XP122_mmgbsa-out_unique.txt > 4BVG_Int_enz_4BVH_AADRP_h2l_small_2-17_mmgbsa-out_merged_v2.txt ------------------------------- command_history_11-04-2013.txt ------------------------------- 135 vi stayalive.sh 136 chmod 700 stayalive.sh 137 ./stayalive.sh 299 cat autogen.sh 837 alias a="~/stayalive.sh" 231 chmod 700 *.py 674 ~/Apps/acepype/acpype.py -h 679 ln -s ~/Apps/acepype/acpype.py acpype 423 cp ../../Ante_RED-1.5.pl ./ 425 perl Ante_RED-1.5.pl dmso.pdb > Ante_RED.log & 437 cp ../../RED-vIII.5.pl ./ 445 m RED-vIII.52.pl 500 vi RED-vIII.5.pl 525 perl RED-vIII.5.pl > RED-vIII.5.log & 528 grep -i firefly RED-vIII.5.pl ------------------------------------------------------- command_history_08-20-2015.txt -------------------------------------------------------- 265 ./calc_RMSDs_bb_per_residue_extra.sh 266 ./summerize_calc_RMSDs_bb_per_residue_extra.sh 353 cat pre-processing_pdb.sh 354 cat run_pbsa.sh 355 vi run_pbsa.sh run2_pbsa.sh 356 cp run_pbsa.sh run2_pbsa.sh 357 vi run2_pbsa.sh 358 ./run2_pbsa.sh 398 chmod 700 run_script.sh_run 399 vi run_script.sh_run 401 ./run_script.sh_run 440 cat run_script.sh_run 442 sed -e 's/210/201/g' run_script.sh_run > ../ID201_comp/run_script.sh_run 459 chmod 700 run_script.sh_run 590 cat run_script.sh_run 592 sed -e 's/210/249/g' run_script.sh_run > /home/plin/home2/work/project01/analysis_schrodinger/sirt3_struct001/set4/ID249_comp/run_script.sh_run 603 cat pre-processing_pdb.sh 608 cat run_pbsa.sh 611 cat run_script.sh_run 745 sed -e 's/249/248/g' run_script.sh_run > ../ID248_comp/run_script.sh_run 760 chmod 700 run_script.sh_run 804 chmod 700 *.sh 806 vi calc_RMSDs_bb_per_residue.sh 807 ./calc_RMSDs_bb_per_residue.sh 827 lt 8.sh 828 lt *.sh 829 mv summerize_calc_RMSDs_bb_per_residue_ref_4FVT2.sh summerize_calc_RMSDs_bb_per_residue.sh 836 cat ./calc_RMSDs_bb_per_residue.sh 837 sed -e 's/4FVT-carbaNAD_set1-/4BVG-set1-/g' ./calc_RMSDs_bb_per_residue.sh > ../4BVG-set1/calc_RMSDs_bb_per_residue.sh 840 lt *.sh 842 cat summerize_calc_RMSDs_bb_per_residue.sh 843 sed -e 's/4FVT-carbaNAD_set1-/4BVG-set1-/g' summerize_calc_RMSDs_bb_per_residue.sh > ../4BVG-set1/summerize_calc_RMSDs_bb_per_residue.sh 877 ./summerize_calc_RMSDs_bb_per_residue.sh 884 cat calc_RMSDs_bb_per_residue.sh 887 vi summerize_calc_RMSDs_bb_per_residue.sh 891 vi ./summerize_calc_RMSDs_bb_per_residue.sh 1061 vi calc_RMSDs_bb_per_residue_extra.sh 1062 vi summerize_calc_RMSDs_bb_per_residue_extra.sh 1074 vi calc_RMSDs_bb_per_residue_extra.sh summerize_calc_RMSDs_bb_per_residue_extra.sh 1115 lt *.sh 1117 cp *.sh *.py 4BVG-s155-178-sp-set1/ 1137 cat summerize_calc_RMSDs_bb_per_residue_extra.sh 1138 cat summerize_calc_RMSDs_bb_per_residue.sh 1161 sed -i -e 's/4BVG-set1-/4FVT-INT-NAM_sp-set1-/g' calc_RMSDs_bb_per_residue.sh 1163 cat summerize_calc_RMSDs_bb_per_residue.sh 1164 sed -i -e 's/4BVG-set1-/4FVT-INT-NAM_sp-set1-/g' summerize_calc_RMSDs_bb_per_residue.sh 1184 lt *.sh 387 ante-MMPBSA.py 454 ante-MMPBSA.py -h 455 ante-MMPBSA.py -p SIRT3_struct001-ID201_comp.prmtop -c SIRT3_struct001-ID201_COM.prmtop -r SIRT3_struct001-ID201_REC.prmtop -l SIRT3_struct001-ID201_LIG.prmtop -s ":WAT,Cl-,CIO,Cs+,IB,K+,Li+,MG2,Na+,Rb+" -n ":NAM" 809 vi ./calc_rmsd_noalign_v2.py 839 lt *.py 841 cp calc_rmsd_noalign_v2.py ../4BVG-set1/ 1085 cat calc_rmsd_noalign_v2.py 1117 cp *.sh *.py 4BVG-s155-178-sp-set1/ 1200 lt *.py 1217 vi calc_rmsd_noalign_v2.py ------------------------------------------- command_history_12-13-2013.txt ------------------------------------------- 360 nohup MMPBSA.py -O -i 4FVT_v1_fixed2_mmpbsa_t02.in -o 4FVT_v1_fixed2_mmpbsa_t02_04md.dat -sp 4FVT_v1_fixed2.prmtop -cp 4FVT_v1a_tern.prmtop -rp 4FVT_v1a_SIRT3_NADp_rec1.prmtop -lp 4FVT_v1a_AceCS2_lig1.prmtop -y 4FVT_v1_fixed2_04md.dcd >& 4FVT_v1_fixed2_mmpbsa_t02_reclig1.log & 699 nohup MMPBSA.py -O -i 4FVT_v1_fixed2_mmpbsa_t02.in -o 4FVT_v1_fixed2_mmpbsa_rec2lig2_07md.dat -sp 4FVT_v1_fixed2.prmtop -cp 4FVT_v1a_tern.prmtop -rp 4FVT_v1a_SIRT3_AceCS2_rec2.prmtop -lp 4FVT_v1a_NADp_lig2.prmtop -y 4FVT_v1_fixed2_07md.dcd >& 4FVT_v1_fixed2_mmpbsa_rec2lig2_07md.log & 708 nohup MMPBSA.py -O -i 4FVT_v1_fixed2_mmpbsa_t02.in -o 4FVT_v1_fixed2_mmpbsa_rec1lig1_07md.dat -sp 4FVT_v1_fixed2.prmtop -cp 4FVT_v1a_tern.prmtop -rp 4FVT_v1a_SIRT3_NADp_rec1.prmtop -lp 4FVT_v1a_AceCS2_lig1.prmtop -y 4FVT_v1_fixed2_07md.dcd >& 4FVT_v1_fixed2_mmpbsa_rec1lig1_07md.log & 817 nohup MMPBSA.py -O -i 4FVT_v1_fixed2_mmpbsa_t02.in -o 4FVT_v1_fixed2_mmpbsa_rec2lig2_07md.dat -sp 4FVT_v1_fixed2.prmtop -cp 4FVT_v1a_tern.prmtop -rp 4FVT_v1a_SIRT3_AceCS2_rec2.prmtop -lp 4FVT_v1a_NADp_lig2.prmtop -y 4FVT_v1_fixed2_07md.dcd >& 4FVT_v1_fixed2_mmpbsa_rec2lig2_07md.log & 845 nohup MMPBSA.py -O -i 4FVT_v1_fixed2_mmpbsa_t02.in -o 4FVT_v1_fixed2_mmpbsa_rec1lig1_07md.dat -sp 4FVT_v1_fixed2.prmtop -cp 4FVT_v1a_tern.prmtop -rp 4FVT_v1a_SIRT3_NADp_rec1.prmtop -lp 4FVT_v1a_AceCS2_lig1.prmtop -y 4FVT_v1_fixed2_07md.dcd >& 4FVT_v1_fixed2_mmpbsa_rec1lig1_07md.log & 1059 nohup MMPBSA.py -O -i 4FVT_v1_fixed2_mmpbsa_igb5.in -o 4FVT_v1_fixed2_mmpbsa_rec1lig1_07md_igb5.dat -sp 4FVT_v1a_fixed2.prmtop -cp 4FVT_v1a_tern.prmtop -rp 4FVT_v1a_SIRT3_NADp_rec1.prmtop -lp 4FVT_v1a_AceCS2_lig1.prmtop -y 4FVT_v1_fixed2_07md.dcd >& 4FVT_v1_fixed2_mmpbsa_rec1lig1_07md_igb5.log & 1062 nohup MMPBSA.py -O -i 4FVT_v1_fixed2_mmpbsa_igb5.in -o 4FVT_v1_fixed2_mmpbsa_rec2lig2_07md_igb5.dat -sp 4FVT_v1a_fixed2.prmtop -cp 4FVT_v1a_tern.prmtop -rp 4FVT_v1a_SIRT3_AceCS2_rec2.prmtop -lp 4FVT_v1a_NADp_lig2.prmtop -y 4FVT_v1_fixed2_07md.dcd >& 4FVT_v1_fixed2_mmpbsa_rec2lig2_07md_igb5.log & 1096 h | grep MMPBSA.py 1097 nohup MMPBSA.py -O -i 4FVT_v1_fixed2_mmpbsa_3traj.in -o 4FVT_v1_fixed2_mmpbsa_rec1lig1_07md_3traj.dat -sp 4FVT_v1a_fixed2.prmtop -cp 4FVT_v1a_SIRT3_AceCS2_rec2.prmtop -rp 4FVT_v1a_SIRT3_rec3.prmtop -lp 4FVT_v1a_AceCS2_lig1.prmtop -y 4FVT_v1_fixed2_07md.dcd -srp 4FVT_v1_SIRT3.prmtop -yr ../4FVT_v1_SIRT3_06md.dcd -slp 4FVT_v1_AceCS2.prmtop -yl 4FVT_v1_AceCS2_04md.dcd >& 4FVT_v1_fixed2_mmpbsa_rec1lig1_07md_3traj.log & 1105 nohup MMPBSA.py -O -i 4FVT_v1_fixed2_mmpbsa_3traj.in -o 4FVT_v1_fixed2_mmpbsa_rec2lig2_07md_3traj.dat -sp 4FVT_v1a_fixed2.prmtop -cp 4FVT_v1a_SIRT3_NADp_rec1.prmtop -rp 4FVT_v1a_SIRT3_rec3.prmtop -lp 4FVT_v1a_NADp_lig2.prmtop -y 4FVT_v1_fixed2_07md.dcd -srp 4FVT_v1_SIRT3.prmtop -yr 4FVT_v1_SIRT3_06md.dcd -slp 4FVT_v1_NADp.prmtop -yl 4FVT_v1a_NADp_05md.dcd >& 4FVT_v1_fixed2_mmpbsa_rec2lig2_07md_3traj.log & 1135 nohup MMPBSA.py -O -i 4FVT_v1_fixed2_mmpbsa_3traj.in -o 4FVT_v1_fixed2_mmpbsa_rec2lig2_07md_3traj.dat -sp 4FVT_v1a_fixed2.prmtop -cp 4FVT_v1a_SIRT3_NADp_rec1.prmtop -rp 4FVT_v1a_SIRT3_rec3.prmtop -lp 4FVT_v1a_NADp_lig2.prmtop -y 4FVT_v1_fixed2_07md.dcd -srp 4FVT_v1_SIRT3.prmtop -yr 4FVT_v1_SIRT3_06md.dcd -slp 4FVT_v1a_NADp.prmtop -yl 4FVT_v1a_NADp_05md.dcd >& 4FVT_v1_fixed2_mmpbsa_rec2lig2_07md_3traj.log & 1164 nohup MMPBSA.py -O -i 4FVT_v1_fixed2_mmpbsa_igb2_v2.in -o 4FVT_v1_fixed2_mmpbsa_rec1lig1_07md_igb2_v2.dat -sp 4FVT_v1a_fixed2.prmtop -cp 4FVT_v1a_tern.prmtop -rp 4FVT_v1a_SIRT3_NADp_rec1.prmtop -lp 4FVT_v1a_AceCS2_lig1.prmtop -y 4FVT_v1_fixed2_07md.dcd >& 4FVT_v1_fixed2_mmpbsa_rec1lig1_07md_igb2_v2.log & 1171 nohup MMPBSA.py -O -i 4FVT_v1_fixed2_mmpbsa_igb2_v2.in -o 4FVT_v1_fixed2_mmpbsa_rec2lig2_07md_igb2_v2.dat -sp 4FVT_v1a_fixed2.prmtop -cp 4FVT_v1a_tern.prmtop -rp 4FVT_v1a_SIRT3_AceCS2_rec2.prmtop -lp 4FVT_v1a_NADp_lig2.prmtop -y 4FVT_v1_fixed2_07md.dcd >& 4FVT_v1_fixed2_mmpbsa_rec2lig2_07md_igb2_v2.log & 553 perl Ante_RED-1.5.pl Int_Part1.pdb > Int001_ante_RED.log 557 vi RED-vIII.52.pl 576 cat RED-vIII.52.pl 584 perl RED-vIII.52.pl >& Int_Part1_RED.log & 592 perl Ante_RED-1.5.pl Int_Part1.pdb > Int001_ante_RED.log 601 perl RED-vIII.52.pl >& Int_Part1_RED.log & 675 vi RED-vIII.52.pl 726 m RED-vIII.52.pl 727 grep JOB1-gam_m1-1.log RED-vIII.52.pl 728 grep JOB1-gam_m1-1 RED-vIII.52.pl 729 grep JOB RED-vIII.52.pl 730 grep JOB1 RED-vIII.52.pl 731 grep JOB1-gam RED-vIII.52.pl 732 m RED-vIII.52.pl 736 perl RED-vIII.52.pl >& Int_Part1_RED2.log & 740 grep 'optimization OUTPUT can not be found' RED-vIII.52.pl 741 m RED-vIII.52.pl 744 perl RED-vIII.52.pl >& Int_Part1_RED2.log & ------------------------------------- command_history.txt_11-21-2013.txt ------------------------------------ 491 vi ~/stayalive.sh 114 vi remove_duplicate.pl 115 chmod 700 remove_duplicate.pl 121 ./remove_duplicate.pl 130 ./remove_duplicate.pl > test.txt 160 ./remove_duplicate.pl 4BVG_enz_h2l_small_02-17-XP99_mmgbsa-out.txt 162 ./remove_duplicate.pl 4BVG_Int_h2l_small_8-12abc-XP103_mmgbsa-out.txt > 4BVG_Int_h2l_small_8-12abc-XP103_mmgbsa-out_unique.txt 163 ./remove_duplicate.pl 4BVG_Int_h2l_small_acid-XP105_mmgbsa-out.txt > 4BVG_Int_h2l_small_acid-XP105_mmgbsa-out_unique.txt 164 ./remove_duplicate.pl 4BVG_enz_h2l_small_acid-XP113_mmgbsa-out.txt > 4BVG_enz_h2l_small_acid-XP113_mmgbsa-out_unique.txt 165 ./remove_duplicate.pl 4BVG_Int_h2l_small_4-7a-XP100_mmgbsa-out.txt > 4BVG_Int_h2l_small_4-7a-XP100_mmgbsa-out_unique.txt 167 cp remove_duplicate.pl merge_hits.pl 168 vi merge_hits.pl 175 ./remove_duplicate.pl 4BVG_enz_h2l_small_20-24-XP112_mmgbsa-out.txt > 4BVG_enz_h2l_small_20-24-XP112_mmgbsa-out_unique.txt 176 ./remove_duplicate.pl 4BVG_Int_h2l_small_20-24-XP104_mmgbsa-out.txt > 4BVG_Int_h2l_small_20-24-XP104_mmgbsa-out_unique.txt 177 ./remove_duplicate.pl 4BVH_AADRP_h2l_small_20-24-XP114_mmgbsa-out.txt > 4BVH_AADRP_h2l_small_20-24-XP114_mmgbsa-out_unique.txt 178 ./merge_hits.pl 4BVG_Int_h2l_small_20-24-XP104_mmgbsa-out_unique.txt 4BVG_enz_h2l_small_20-24-XP112_mmgbsa-out_unique.txt 4BVH_AADRP_h2l_small_20-24-XP114_mmgbsa-out_unique.txt 239 ./remove_duplicate.pl 4BVG_Int_h2l_small_20-24-XP104_mmgbsa-out.txt 243 ./remove_duplicate.pl 4BVG_Int_h2l_small_20-24-XP104_mmgbsa-out.txt > 4BVG_Int_h2l_small_20-24-XP104_mmgbsa-out_unique.txt 246 ./merge_hits.pl 4BVG_Int_h2l_small_20-24-XP104_mmgbsa-out_unique.txt 4BVG_enz_h2l_small_20-24-XP112_mmgbsa-out_unique.txt 4BVH_AADRP_h2l_small_20-24-XP114_mmgbsa-out_unique.txt 247 ./merge_hits.pl 4BVG_Int_h2l_small_20-24-XP104_mmgbsa-out_unique.txt 4BVG_enz_h2l_small_20-24-XP112_mmgbsa-out_unique.txt 4BVH_AADRP_h2l_small_20-24-XP114_mmgbsa-out_unique.txt > 4BVG_Int_enz_4BVH_AADRP_h2l_small_20-24_mmgbsa-out_merged.txt 262 ./remove_duplicate.pl 4BVG_enz_h2l_small_02-17-XP99_mmgbsa-out.txt > 4BVG_enz_h2l_small_02-17-XP99_mmgbsa-out_unique.txt2 269 ./remove_duplicate.pl 4BVG_Int_h2l_smal02-17-prime_mmgbsa-out.txt > 4BVG_Int_h2l_smal02-17-prime_mmgbsa-out_unique.txt 270 ./remove_duplicate.pl 4BVG_Int_h2l_small_8-12abc-XP103_mmgbsa-out.txt > 4BVG_Int_h2l_small_8-12abc-XP103_mmgbsa-out_unique.txt 271 ./remove_duplicate.pl 4BVG_Int_h2l_small_acid-XP105_mmgbsa-out.txt > 4BVG_Int_h2l_small_acid-XP105_mmgbsa-out_unique.txt 272 ./remove_duplicate.pl 4BVG_enz_h2l_small_acid-XP113_mmgbsa-out.txt > 4BVG_enz_h2l_small_acid-XP113_mmgbsa-out_unique.txt 273 ./remove_duplicate.pl 4BVG_Int_h2l_small_4-7a-XP100_mmgbsa-out.txt > 4BVG_Int_h2l_small_4-7a-XP100_mmgbsa-out_unique.txt 275 ./remove_duplicate.pl 4BVH_AADRP_h2l_small_20-24-XP114_mmgbsa-out.txt > 4BVH_AADRP_h2l_small_20-24-XP114_mmgbsa-out_unique.txt 276 ./remove_duplicate.pl 4BVG_Int_h2l_small_20-24-XP104_mmgbsa-out.txt > 4BVG_Int_h2l_small_20-24-XP104_mmgbsa-out_unique.txt 277 ./remove_duplicate.pl 4BVG_enz_h2l_small_20-24-XP112_mmgbsa-out.txt > 4BVG_enz_h2l_small_20-24-XP112_mmgbsa-out_unique.txt 280 ./merge_hits.pl 4BVG_Int_h2l_smal02-17-prime_mmgbsa-out_unique.txt 4BVG_enz_h2l_small_02-17-XP99_mmgbsa-out_unique.txt > 4BVG_Int_enz_h2l_smal02-17_mmgbsa-out_merged.txt 282 ./merge_hits.pl 4BVG_Int_h2l_small_acid-XP105_mmgbsa-out_unique.txt 4BVG_enz_h2l_small_acid-XP113_mmgbsa-out_unique.txt > 4BVG_Int_enz_h2l_small_acid_mmgbsa-out_merged.txt 875 ./remove_duplicate.pl 4BVH_AADRP_h2l_small-2-17_XP122_mmgbsa-out.txt > 4BVH_AADRP_h2l_small-2-17_XP122_mmgbsa-out_unique.txt 876 ./remove_duplicate.pl 4BVG_enz_h2l_small_4-7a_XP110_mmgbsa-out.txt > 4BVG_enz_h2l_small_4-7a_XP110_mmgbsa-out_unique.txt 877 ./remove_duplicate.pl 4BVG_enz_h2l_small_8-12abc_XP127_mmgbsa-out.txt > 4BVG_enz_h2l_small_8-12abc_XP127_mmgbsa-out_unique.txt 878 ./merge_hits.pl 4BVG_Int_h2l_small_4-7a-XP100_mmgbsa-out_unique.txt 4BVG_enz_h2l_small_4-7a_XP110_mmgbsa-out_unique.txt 879 ./merge_hits.pl 4BVG_Int_h2l_small_4-7a-XP100_mmgbsa-out_unique.txt 4BVG_enz_h2l_small_4-7a_XP110_mmgbsa-out_unique.txt > 4BVG_Int_enz_h2l_small_4-7a_mmgbsa-out_merged.txt 881 ./merge_hits.pl 4BVG_Int_h2l_small_8-12abc-XP103_mmgbsa-out_unique.txt 4BVG_enz_h2l_small_8-12abc_XP127_mmgbsa-out_unique.txt > 4BVG_Int_enz_h2l_small_8-12abc_mmgbsa-out_merged.txt 882 ./merge_hits.pl 4BVG_Int_h2l_smal02-17-prime_mmgbsa-out_unique.txt 4BVG_enz_h2l_small_02-17-XP99_mmgbsa-out_unique.txt 4BVH_AADRP_h2l_small-2-17_XP122_mmgbsa-out_unique.txt > 4BVG_Int_enz_4BVH_AADRP_h2l_small_2-17_mmgbsa-out_merged.txt 959 ./remove_duplicate.pl 4BVH_AADRP_h2l_small-acids_XP125_mmgbsa-out.txt > 4BVH_AADRP_h2l_small-acids_XP125_mmgbsa-out_unique.txt 961 ./merge_hits.pl 4BVG_Int_h2l_small_acid-XP105_mmgbsa-out_unique.txt 4BVG_enz_h2l_small_acid-XP113_mmgbsa-out_unique.txt 4BVH_AADRP_h2l_small-acids_XP125_mmgbsa-out_unique.txt > 4BVG_Int_enz_4BVH_AADRP_h2l_small_small-acids_mmgbsa-out_merged.txt 1014 ./remove_duplicate.pl 4BVH_AADRP_h2l_small-4-7a_XP124_mmgbsa-out.txt > 4BVH_AADRP_h2l_small-4-7a_XP124_mmgbsa-out_unique.txt 1015 ./merge_hits.pl 4BVG_Int_h2l_small_4-7a-XP100_mmgbsa-out_unique.txt 4BVG_enz_h2l_small_4-7a_XP110_mmgbsa-out_unique.txt 4BVH_AADRP_h2l_small-4-7a_XP124_mmgbsa-out_unique.txt > 4BVG_Int_enz_4BVH_AADRP_h2l_small-4-7a_mmgbsa-out_merged.txt -------------------------------------------- command_history_01-24-2014.txt ------------------------------------------- 1278 cat link_prmtop_dcd.sh 1300 ./run_script.sh 1373 cat run_script.sh 1407 cp run_script.sh run1/ 1409 vi run_script.sh 771 nohup MMPBSA.py -O -i 4FVT_v1_fixed2_mmpbsa_igb5_1.in -o 4FVT_v1_fixed2_mmpbsa_rec2lig2_01min.dat -sp 4FVT_v1_fixed2.prmtop -cp 4FVT_v1a_tern.prmtop -rp 4FVT_v1a_SIRT3_AceCS2_rec2.prmtop -lp 4FVT_v1a_NADp_lig2.prmtop -y ../4FVT_v1_fixed2_01min.dcd >& 4FVT_v1_fixed2_mmpbsa_rec2lig2_01min.log & 809 nohup MMPBSA.py -O -i 4FVT_v1_fixed2_mmpbsa_igb1_1.in -o 4FVT_v1_fixed2_mmpbsa_rec2lig2_01min_igb1.dat -sp 4FVT_v1a_fixed2.prmtop -cp 4FVT_v1a_tern.prmtop -rp 4FVT_v1a_SIRT3_AceCS2_rec2.prmtop -lp 4FVT_v1a_NADp_lig2.prmtop -y ../4FVT_v1_fixed2_01min.dcd >& 4FVT_v1_fixed2_mmpbsa_rec2lig2_01min_igb1.log & 858 h | grep MMPBSA.py 859 nohup MMPBSA.py -O -i 4FVT_v1_fixed2_mmpbsa_igb1_1.in -o 4FVT_v1_fixed2_mmpbsa_rec2lig2_08md_igb1.dat -sp 4FVT_v1a_fixed2.prmtop -cp 4FVT_v1a_tern.prmtop -rp 4FVT_v1a_SIRT3_AceCS2_rec2.prmtop -lp 4FVT_v1a_NADp_lig2.prmtop -y 4FVT_v1_fixed2_08md.dcd >& 4FVT_v1_fixed2_mmpbsa_rec2lig2_08md_igb1.log & 873 nohup MMPBSA.py -O -i 4FVT_v1_fixed2_mmpbsa_pb_1.in -o 4FVT_v1_fixed2_mmpbsa_rec2lig2_08md_pb_1.dat -sp 4FVT_v1a_fixed2.prmtop -cp 4FVT_v1a_tern.prmtop -rp 4FVT_v1a_SIRT3_AceCS2_rec2.prmtop -lp 4FVT_v1a_NADp_lig2.prmtop -y 4FVT_v1_fixed2_08md.dcd >& 4FVT_v1_fixed2_mmpbsa_rec2lig2_08md_pb_1.log & 892 nohup MMPBSA.py -O -i 4FVT_v1_fixed2_mmpbsa_pb_1.in -o 4FVT_v1_fixed2_mmpbsa_rec1lig1_08md_1.dat -sp 4FVT_v1_fixed2.prmtop -cp 4FVT_v1a_tern.prmtop -rp 4FVT_v1a_SIRT3_NADp_rec1.prmtop -lp 4FVT_v1a_AceCS2_lig1.prmtop -y 4FVT_v1_fixed2_08md.dcd >& 4FVT_v1_fixed2_mmpbsa_rec1lig1_08md_1.log & 932 m RED-vIII.52.pl 945 cp ../Ante_RED-1.5.pl ./ 946 perl Ante_RED-1.5.pl isoNAM_1.pdb 1336 vi calc_conv.pl 1337 scp -rp plin@pmcat-gpu1:/home/plin/work/project01/MD_isoNAM/mmpbsa_rec3lig3_md_pbgbsa/calc_conv.pl ./ 1339 ./calc_conv.pl AcCS2_MM-GBSA_2ns.dat 1340 ./calc_conv.pl AcCS2_MM-PBSA_2ns.dat 1347 cp ../mmpbsa_rec1lig1_md_pbgbsa/calc_conv.pl ./ ------------------------------------- command_history_04-09-2014.txt --------------------------------- 124 ./batch_rename.sh 136 vi batch_rename.sh 178 cp run_script.sh run_G_comp.sh 179 vi run_G_comp.sh 181 ./run_G_comp.sh 193 ./run_G_comp.sh r 200 vi ./run_G_comp.sh 203 cp ./run_G_comp.sh ../../MD_2H4F_tern/mmpbsa_rec2lig2_md_pbgbsa/ 208 diff ./run_G_comp.sh ../../MD_2H4F_tern/mmpbsa_rec2lig2_md_pbgbsa/run_G_comp.sh 209 m ./run_G_comp.sh 210 cp ./run_G_comp.sh ../../MD_4FVT_NAM/mmpbsa_rec2lig2_md_pbgbsa/ 224 cp run_G_comp_v2.sh calc_conv.pl ../mmpbsa_rec3lig3_md_pbgbsa/ 227 ./run_G_comp_v2.sh 279 vi create_snapshots.sh 280 chmod 700 create_snapshots.sh 283 ./create_snapshots.sh 287 vi create_snapshots.sh 290 cp create_snapshots.sh /home/plin/work/project01/MD_SIRT3_NADp/ 364 vi res_energy_decomp_run00.sh 365 ./res_energy_decomp_run00.sh 366 ./res_energy_decomp_run01.sh 368 vi ./res_energy_decomp_run01.sh 369 ./res_energy_decomp_run01.sh 372 vi res_energy_decomp_run02a.sh 373 ./res_energy_decomp_run02a.sh 378 vi res_energy_decomp_run02a.sh 380 vi res_energy_decomp_run02a.sh 384 cat res_energy_decomp_run03.sh 385 ./res_energy_decomp_run03.sh 394 cat MD_2H4F_NAM/processing_2H4F_NAM_pdb.sh 395 cat MD_2H4F_tern/processing_2H4F_tern_pdb.sh 396 cat MD_4FVT_NAM/create_snapshots.sh 397 cp MD_2H4F_NAM/processing_2H4F_NAM_pdb.sh MD_4FVT_MNA/ 471 cat run_G_comp_v2.sh 474 cp calc_conv.pl run_G_comp_v2.sh ../../MD_4FVT_MNA/mmpbsa_rec2lig2_md_pbgbsa/ 510 vi run_script.sh 511 ./run_script.sh 554 vi processing_4FVT_MNA_pdb.sh 557 mv processing_4FVT_MNA_pdb.sh processing_4KXQ_tern_pdb.sh 558 ./processing_4KXQ_tern_pdb.sh 4KXQ_AcP53_NADp_tern_2.pdb 560 vi processing_4KXQ_tern_pdb.sh 561 ./processing_4KXQ_tern_pdb.sh 4KXQ_AcP53_NADp_tern_2.pdb 567 cat processing_4KXQ_tern_pdb.sh 664 cp run_script.sh ../mmpbsa_rec3lig3_md_pbgbsa/ 700 cp run_script.sh ../mmpbsa_rec1lig1_md_pbgbsa/ 712 vi run_G_comp_v2.sh 716 vi run_G_comp_v2.sh 717 ./run_G_comp_v2.sh 721 cp calc_conv.pl run_G_comp_v2.sh ../mmpbsa_rec3lig3_md_pbgbsa/ 727 ./run_G_comp_v2.sh 761 cp processing_4FVT_MNA_pdb.sh ../MD_4KXQ_tern 886 cat run_script.sh 887 cp run_script.sh ../../MD_4FVT_MNA/mmpbsa_rec2lig2_md_pbgbsa 1058 cat run_script.sh 1059 ./run_script.sh 1070 vi run_G_comp_v2.sh 1074 ./run_G_comp_v2.sh >& Component_analysis.dat & 988 cat plot_solution.py 1035 vim mysqrt.py 204 cp ./calc_conv.pl ../../MD_2H4F_tern/mmpbsa_rec2lig2_md_pbgbsa/ 207 diff ./calc_conv.pl ../../MD_2H4F_tern/mmpbsa_rec2lig2_md_pbgbsa/calc_conv.pl 211 cp ./calc_conv.pl ../../MD_4FVT_NAM/mmpbsa_rec2lig2_md_pbgbsa/ 224 cp run_G_comp_v2.sh calc_conv.pl ../mmpbsa_rec3lig3_md_pbgbsa/ 474 cp calc_conv.pl run_G_comp_v2.sh ../../MD_4FVT_MNA/mmpbsa_rec2lig2_md_pbgbsa/ 483 cat calc_conv.pl 721 cp calc_conv.pl run_G_comp_v2.sh ../mmpbsa_rec3lig3_md_pbgbsa/ 925 m prepare_amber.pl 951 ./prepare_amber.pl 952 ./bin/prepare_amber.pl 954 nohup ./bin/prepare_amber.pl 4BVG_Int4c_small_1_dockposes.mol2 4BVG_Int_fixed2.pdb >& testZn2_results.log & --------------------------------------------- command_history_04-28-2014.txt --------------------------------------------- 188 ./run_G_comp.sh 193 ./run_G_comp.sh r 198 vi ./run_G_comp.sh 203 cp ./run_G_comp.sh ../../MD_2H4F_tern/mmpbsa_rec2lig2_md_pbgbsa/ 208 diff ./run_G_comp.sh ../../MD_2H4F_tern/mmpbsa_rec2lig2_md_pbgbsa/run_G_comp.sh 209 m ./run_G_comp.sh 210 cp ./run_G_comp.sh ../../MD_4FVT_NAM/mmpbsa_rec2lig2_md_pbgbsa/ 224 cp run_G_comp_v2.sh calc_conv.pl ../mmpbsa_rec3lig3_md_pbgbsa/ 227 ./run_G_comp_v2.sh 279 vi create_snapshots.sh 280 chmod 700 create_snapshots.sh 281 ./create_snapshots.sh 290 cp create_snapshots.sh /home/plin/work/project01/MD_SIRT3_NADp/ 364 vi res_energy_decomp_run00.sh 365 ./res_energy_decomp_run00.sh 366 ./res_energy_decomp_run01.sh 368 vi ./res_energy_decomp_run01.sh 369 ./res_energy_decomp_run01.sh 372 vi res_energy_decomp_run02a.sh 373 ./res_energy_decomp_run02a.sh 378 vi res_energy_decomp_run02a.sh 380 vi res_energy_decomp_run02a.sh 384 cat res_energy_decomp_run03.sh 385 ./res_energy_decomp_run03.sh 394 cat MD_2H4F_NAM/processing_2H4F_NAM_pdb.sh 395 cat MD_2H4F_tern/processing_2H4F_tern_pdb.sh 396 cat MD_4FVT_NAM/create_snapshots.sh 397 cp MD_2H4F_NAM/processing_2H4F_NAM_pdb.sh MD_4FVT_MNA/ 471 cat run_G_comp_v2.sh 473 cat run_G_comp_v2.sh 474 cp calc_conv.pl run_G_comp_v2.sh ../../MD_4FVT_MNA/mmpbsa_rec2lig2_md_pbgbsa/ 511 ./run_script.sh 517 vi run_script.sh 554 vi processing_4FVT_MNA_pdb.sh 557 mv processing_4FVT_MNA_pdb.sh processing_4KXQ_tern_pdb.sh 558 ./processing_4KXQ_tern_pdb.sh 4KXQ_AcP53_NADp_tern_2.pdb 560 vi processing_4KXQ_tern_pdb.sh 561 ./processing_4KXQ_tern_pdb.sh 4KXQ_AcP53_NADp_tern_2.pdb 567 cat processing_4KXQ_tern_pdb.sh 664 cp run_script.sh ../mmpbsa_rec3lig3_md_pbgbsa/ 700 cp run_script.sh ../mmpbsa_rec1lig1_md_pbgbsa/ 712 vi run_G_comp_v2.sh 717 ./run_G_comp_v2.sh 721 cp calc_conv.pl run_G_comp_v2.sh ../mmpbsa_rec3lig3_md_pbgbsa/ 761 cp processing_4FVT_MNA_pdb.sh ../MD_4KXQ_tern 886 cat run_script.sh 887 cp run_script.sh ../../MD_4FVT_MNA/mmpbsa_rec2lig2_md_pbgbsa 1062 cp processing_4BV3_tern_pdb.sh ../MD_4BVH_AADPR_OCZ/ 1076 vi gpu-free.sh 1163 vi processing_4BVH_tern_pdb.sh 988 cat plot_solution.py 204 cp ./calc_conv.pl ../../MD_2H4F_tern/mmpbsa_rec2lig2_md_pbgbsa/ 207 diff ./calc_conv.pl ../../MD_2H4F_tern/mmpbsa_rec2lig2_md_pbgbsa/calc_conv.pl 211 cp ./calc_conv.pl ../../MD_4FVT_NAM/mmpbsa_rec2lig2_md_pbgbsa/ 224 cp run_G_comp_v2.sh calc_conv.pl ../mmpbsa_rec3lig3_md_pbgbsa/ 474 cp calc_conv.pl run_G_comp_v2.sh ../../MD_4FVT_MNA/mmpbsa_rec2lig2_md_pbgbsa/ 708 cat calc_conv.pl 721 cp calc_conv.pl run_G_comp_v2.sh ../mmpbsa_rec3lig3_md_pbgbsa/ 925 m prepare_amber.pl 951 ./prepare_amber.pl 952 ./bin/prepare_amber.pl 954 nohup ./bin/prepare_amber.pl 4BVG_Int4c_small_1_dockposes.mol2 4BVG_Int_fixed2.pdb >& testZn2_results.log & 1132 cat ../RED-vIII.52.pl 1134 perl ../RED-vIII.5.pl >& RED-vIII.5.log &