RSK: PLOS one paper MD trajectory (SiRt3 - Ternary complex- 4FVT values reported in paper) and analysis carried out by ping is located in
/home2/plin/work/project01/MD_4FVT_tern/mmpbsa_rec2lig2_md_pbgbsa
Updated on 7th Mar, 2016
RSK: This document contains annotation pertaining to the location of raw data for the KT document
(Sidechain prediction validation set 1 PL RC)
Sidechain prediction validation set 1 PL RC PL _Vijayan_annotated.docx
Update on 4th Mar, 2016
Script List_annotated_vijayan.doc
manuscript computational section excerpts and tasks.docx
RSK:
documents contain
a brief summary on the functionality and location of all the scripts provided during KT
" manuscript computational section excerpts and tasks" document contain the mapped location of the raw data
Update on 11th Nov, 2015
RC: Is most of the third party source code in /usr/src? Is amber source there?
AS: Most of the third party source code in /usr/src. amber source is also under /usr/src/
several Schrodinger python scripts including ifd are in /usr/src/Schrodinger2014/psp-v37013/bin/Linux-x86_64/
RC: Let me know whether you are able to access files on the cluster/gpu node directly from pings desktop - ie is there any sort of shared directory - or, does one have to log in to gpu node to access those files.
AS: I have checked smb.conf file, there is no shared directory between desktop and cluster. There is no FTP configuration in pmcat-gpu1. We have to log in to pmcat-gpu1 node to access those files.
1. Some questions with answers from Dr. Ping Lin regarding Licence Server, Schrodinger, In-house and Third Party Software.
Question List.doc
2. List of data files and project folder of cluster.
List of data files and Project folder .doc
3. List of Schrodinger executables
List of source and executables.doc
4. Indicated which were developed in-house and which were written by third parties
In-house-and-third-party-software.doc
5. List of scripts used/developed by PL
Script List.doc
6. Command history mentioned in scripts directory and putted all the history related to each script in a text file.
commands_history.txt
7. Checked -h option for calc_rmsd_noalign_v2.py
RMSD Script -h.doc
8. Checked -h option for all scripts.
Script-List.doc
9. While the job is running, issued the license server STAT command Ping mentioned and see how many tokens were used by the job.
STAT.doc