Lig pb energy value nan

155 views
Skip to first unread message

Amal_porto

unread,
Jun 13, 2018, 5:31:49 AM6/13/18
to g_mmpbsa Mailing List
Dear Users

I am totally new to gromacs and g_mmpbsa software. I am trying to calculate binding free energy of
carbon-nanotube and protein complex. I find CNT PB energy of the system is always nan. However, I
followed all suggestions which were previously discussed like pbc and error in input files, but could not
solve the problem. Most importantly, the CNT atoms dont have any charge which could be a source of
error. I am eagerly waiting for your suggestions regarding this error.

please see the following link for input files
https://drive.google.com/open?id=180FKxZjQj4yfrd5BEP3kgxgEB1kIwqnY

Thanks

g_mmpbsa Mailing List

unread,
Jun 15, 2018, 9:15:48 AM6/15/18
to g_mmpbsa Mailing List

Polar solvation energy requires partial atomic charge on atoms. That may be the cause of nan value in your case.

h.mosa...@gmail.com

unread,
Aug 25, 2020, 2:32:40 PM8/25/20
to g_mmpbsa Mailing List
Hi how solve it? if use polar=no, I get this error after run pyhton:

polar.xvg not found

h.mosa...@gmail.com

unread,
Aug 29, 2020, 4:39:48 AM8/29/20
to g_mmpbsa Mailing List
Hi
solved your problem?
Reply all
Reply to author
Forward
0 new messages