[gmx-users] Re: charmm, cmap and gromacs 4.1
Justin A. Lemkul
jalemkul at vt.edu
Wed Jan 13 01:13:20 CET 2010
> > Hello. Thank you for the git repository tip, but I don't think it
> > out.
> > I tried using "git clone git://git.gromacs.org/gromacs.git
> Did you do git pull?
> > From the
> > gromacs directory that git created I ran "./bootstrap" and then
> > .....etc.
> > I inserted the ffcharmm files into the ~GROMACSPATH/top directory
> and edited
> > the FF.dat file to include a eleventh line with the ffcharmm27
> > Finally, when I ran pdb2gmx and chose ffcharmm27 as a forcefield
> > gave the following error:
> > Fatal error:
> > in .rtp file in residue cmap at line:
> > -C N CA C +N
> >>> I wanted to use charmm forcefield on gromacs (am using 4.07)
> but when I
> >> try
> >>> using this forcefield gromacs tells me that there is a problem
> with CMAP.
> >> I
> >>> read that gromacs 4.1 is coming with charmm forcefield as well.
> If that
> >> is
> >>> true, when is gromacs 4.1 coming and how can I use charmm FF
> with gromacs
> >>> for now?
> >> The code supporting CHARMM is in git master (see
> >> http://www.gromacs.org/Developer_Zone/Git/Git_Tutorial) and
> will, as you
> >> say, be included in version 4.1. Download CHARMM force filed
> files v1.1 from
> >> http://www.dbb.su.se/user:bjelkmar/ffcharmm. They will, of
> course, also be
> >> included with 4.1.
> >> Actually, I got the notification yesterday that a paper
> describing this
> >> implementation will be published in JCTC.
> >>> Would it be better to wait for gromacs 4.1?
> >> There might be some minor changes until 4.1 but the current
> (CHARMM-) code
> >> (in git master) is tested and is working well. Once version 4.1
> is released
> >> I would recommend you to update to that version.
> Yes, I did git pull and the output is this:
> remote: Counting objects: 9, done.
> remote: Compressing objects: 100% (5/5), done.
> remote: Total 5 (delta 4), reused 0 (delta 0)
> Unpacking objects: 100% (5/5), done.
> >From git://git.gromacs.org/gromacs <http://git.gromacs.org/gromacs>
> c358dce..b493dbb master -> origin/master
> Already up-to-date.
> Still charmm does not work. Is there something wrong about the way I
> included the forcefield files in the top directory, should I have
> changed something else?
Have you used the right executable? For instance, where did you install the git
version of Gromacs? Are you using instead another version? I tested the git
version today with CMAP support and it worked fine.
Justin A. Lemkul
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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