VMD-L Mailing List

From: Lalit (upmunyu_at_gmail.com)
Date: Mon Jun 06 2011 - 18:19:21 CDT

Hi All,

I am interested in using gromacs utilities for analysis with {.dcd, .psf}
files. One do need to have {.tpr} file for some tools, eg., for g_density.

I am following this link from NAMD mailing list:

http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l/14046.html

As suggest, by Axel, I was able to get the {.top} file.

However, when I used gromacs's "grompp" command:

$ grompp -f minim1.mdp -c BL1_only.pdb -p BL1_only.top -o BL1_only.tpr

I was returned with an error like this:

-------------------------------------------------------
Program grompp, VERSION 4.5.4
Source code file:
/home/mandrake/rpm/BUILD/gromacs-4.5.4/src/kernel/grompp.c, line: 175

Fatal error:
The largest charge group contains 140 atoms. The maximum is 32.
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------

I am searching gromacs mailing list and still looking for an answer. I am
also asking them about this error.

However, I feel like, is there something can be done on {.top} generating
step? I tend to think to resolve this error more through NAMD/VMD point of
view rather then going deep into Gromacs way of thinking and de-bugging.

Please suggest and help.

Thanks a lot,
--- Lalit

p.s.: All relevant files: BL1_only.pdb; BL1_only.psf; BL1_only.top &
minim1.mdp can be downloaded from:

http://lalitpkc.phy.uic.edu/~lalit/GROMACS_files