VMD-L Mailing List
From: Lalit (upmunyu_at_gmail.com)
Date: Mon Jun 06 2011 - 18:19:21 CDT
- Next message: Axel Kohlmeyer: "Re: topotools {.top} for Gromacs {.tpr} generation"
- Previous message: Axel Kohlmeyer: "Re: topotools {.top} for Gromacs {.tpr} generation"
- Next in thread: Axel Kohlmeyer: "Re: topotools {.top} for Gromacs {.tpr} generation"
- Reply: Axel Kohlmeyer: "Re: topotools {.top} for Gromacs {.tpr} generation"
- Reply: Axel Kohlmeyer: "Re: topotools {.top} for Gromacs {.tpr} generation"
- Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] [ attachment ]
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
- Next message: Axel Kohlmeyer: "Re: topotools {.top} for Gromacs {.tpr} generation"
- Previous message: Axel Kohlmeyer: "Re: topotools {.top} for Gromacs {.tpr} generation"
- Next in thread: Axel Kohlmeyer: "Re: topotools {.top} for Gromacs {.tpr} generation"
- Reply: Axel Kohlmeyer: "Re: topotools {.top} for Gromacs {.tpr} generation"
- Reply: Axel Kohlmeyer: "Re: topotools {.top} for Gromacs {.tpr} generation"
- Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] [ attachment ]