Hi All,
At this time, I am very much interested in using gromacs utilities for
analysis with {.dcd, .psf} files. Especially, eg., for g_density.
Primarily, I use NAMD/VMD for my work.
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:
* * *
Back Off! I just backed up mdout.mdp to ./#mdout.mdp.4#
Generated 231 of the 231 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 0.5
Generated 231 of the 231 1-4 parameter combinations
Excluding 3 bonded neighbours molecule type 'molecule0'
Excluding 3 bonded neighbours molecule type 'molecule1'
NOTE 1 [file BL1_only.top, line 1880]:
System has non-zero total charge: -5.999999e+01
-------------------------------------------------------
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
-------------------------------------------------------
My system is a mixed bilayer with negative 60 charge on it.
I am searching gromacs mailing list and still looking for an answer.
Is there a way to use g_density with my set of files - {.psf, .pdb, .dcd} ?
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
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