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dptech-corp / Uni-GBSA

An automatic workflow to perform MM/GB(PB)SA calculations from force field building, and structure optimization to free energy calculation.
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The resulting .xtc file from unigbsa-md had not water molecules and ions. #58

Open Tangbbmc opened 1 month ago

Tangbbmc commented 1 month ago

The resulting .xtc file from unigbsa-md had not water molecules and ions. How to include water molecules and ions in .xtc file. Moreover, when processing pbc with unigbsa-pbc command, I received the following error:

(gbsa) dell@dell-OptiPlex-Tower-Plus-7010:~/Downloads/Uni-GBSA-master/example/1ceb$ unigbsa-pbc -s md.tpr -f md-pbc.xtc -o md-nopbc.xtc -n index.ndx gmx trjconv -s md.tpr -n index.ndx -f md-pbc.xtc -o md-pbc-1.xtc -pbc mol -ur compact >> /dev/null 2>&1 << EOF output EOF Traceback (most recent call last): File "/home/dell/anaconda3/envs/gbsa/bin/unigbsa-pbc", line 8, in sys.exit(PBC_main()) ^^^^^^^^^^ File "/home/dell/anaconda3/envs/gbsa/lib/python3.12/site-packages/unigbsa/CLI.py", line 31, in PBC_main process_pbc(trajfile, tprfile, indexfile=indexfile, outfile=outfile) File "/home/dell/anaconda3/envs/gbsa/lib/python3.12/site-packages/unigbsa/utils.py", line 117, in process_pbc raise Exception('Process pbc error: see the %s file for details'%logfile) Exception: Process pbc error: see the /dev/null file for details

Aunity commented 4 weeks ago

You can save all files during the MD process by adding the -verbose parameter. And the outdir/complex.GMX/md.xtc is the trajectory contains the water molecules and ions. As for the error you mentioned, could you please provide all the files you run（md.tpr, md-pbc.xtc and index.ndx）?

Tangbbmc commented 4 weeks ago

Ok. I am very glad to receive your reply! Could you further introduce the differences among md.xtc, md-pbc.xtc, and traj_comx.xtc? Does traj_comx.txc have removed PBC?

发件人：Maohua Yang @.> 发送日期：2024-10-25 16:34:52 收件人：dptech-corp/Uni-GBSA @.> 抄送人：Wanggang @.>,Author @.> 主题：Re: [dptech-corp/Uni-GBSA] The resulting .xtc file from unigbsa-md had not water molecules and ions. (Issue #58)

You can save all files during the MD process by adding the -verbose parameter. And the outdir/complex.GMX/md.xtc is the trajectory contains the water molecules and ions. As for the error you mentioned, could you please provide all the files you run（md.tpr, md-pbc.xtc and index.ndx）? — Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you authored the thread.Message ID: @.***>

Aunity commented 4 weeks ago

The md.xtc file is the original output trajectory file of the md production. The md-pbc.xtc and the traj_comx.xtc file are the same file in different floder and name. The md-pbc.xtc file is the md.xtc file with PBC removed, and the traj_comx.xtc is a copy of md-pbc.xtc file.

Tangbbmc commented 4 weeks ago

I see. Thank you very much for your advice.

发件人：Maohua Yang @.> 发送日期：2024-10-25 21:54:23 收件人：dptech-corp/Uni-GBSA @.> 抄送人：Wanggang @.>,Author @.> 主题：Re: [dptech-corp/Uni-GBSA] The resulting .xtc file from unigbsa-md had not water molecules and ions. (Issue #58)

The md.xtc file is the original output trajectory file of the md production. The md-pbc.xtc and the traj_comx.xtc file are the same file in different floder and name. The md-pbc.xtc file is the md.xtc file with PBC removed, and the traj_comx.xtc is a copy of md-pbc.xtc file. — Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you authored the thread.Message ID: @.***>