[gmx-users] Re: Charmm port files for Gromacs
bjelkmar at cbr.su.se
Tue Apr 6 09:34:31 CEST 2010
I answer to the gmx-users mailing list and I would be pleased if further correspondence is done there.
It's an installation issue because the CMAP directive is not recognized by pdb2gmx. Seems like you are running version 4.0.7 and that is then the explanation. You need to run with the developing version (because it is has not been released yet) from git to run with CHARMM. There're installation instructions on the gromacs webpage.
Worth to note:
1. more information about the port is available in paper by yours sincerely and coworkers (Bjelkmar et al. Journal of Chemical Theory and Computation, 2010)
2. the force field format has been changed and the most recent version of the force field (complying to this new format) was added to the source. I.e. you should use those files (not the ffcharmm27* files from my homepage).
5 apr 2010 kl. 17.51 skrev Smiruthi Ramasubramanian:
> Hi Pär,
> I've been testing the charmm27 forcefield and keep getting this error:
> Program pdb2gmx, VERSION 4.0.7
> Source code file: resall.c, line: 344
> Fatal error:
> in .rtp file in residue cmap at line:
> -C N CA C +N
> I couldn't find a plausible solution in the gmx forums and was wondering if there was a problem in the installation. I am not using ACE or other capping residues in the pdb.
> On Thu, Mar 18, 2010 at 6:00 AM, Pär Bjelkmar <bjelkmar at cbr.su.se> wrote:
> Hello Smiruthi,
> Nice to hear that you're interested in the port. First, you need to run with the git head version (see instructions on my page www.dbb.su.se/User:bjelkmar/Ffcharmm or on gromacs.org). Since about one month, the version of the force field (version 1.1) on this homepage has not been working with git head because the force field format was changed in GROMACS. Yesterday, I committed the updated version of the CHARMM parameters to the version-tracking program (git) in the head branch so it should work now. However, this is still a somewhat work-in-progress force field port (especially in the nucleic acid part) and there _might_ be changes (although minor ones for sure) until GROMACS 4.1 is released. The protein and lipid parts should be fairly safe to use though.
> Regards and good luck,
> Pär Bjelkmar
> 16 mar 2010 kl. 20.20 skrev Smiruthi Ramasubramanian:
>> Hi Pär,
>> I am a Phd student in Rudy Lab (http://rudylab.wustl.edu/) at Wustl. We are working on comparing NAMD and Gromacs umbrella sampling related to passage of ions through membrane proteins. Could you please send me the Charmm port files listed in http://www.dbb.su.se/User:Bjelkmar/Ffcharmm . Unfortunately, I keep getting "Internal Error" and I am not sure if it is a problem at our end or if your server is temporarily down.
>> I apologize for any inconvenience and appreciate the help.
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