[gmx-users] Re: Re: charmm, cmap and gromacs 4.1

[Stefan Hoorman]

> Message: 1
> Date: Tue, 12 Jan 2010 19:13:20 -0500
> From: "Justin A. Lemkul" <jalemkul at vt.edu>
> Subject: Re: [gmx-users] Re: charmm, cmap and gromacs 4.1
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <4B4D1020.3060801 at vt.edu>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
>
>
> stefhoor wrote:
> > Hi,
> >
> >
> >      > Hello. Thank you for the git repository tip, but I don't think it
> >     worked
> >      > out.
> >      > I tried using "git clone git://git.gromacs.org/gromacs.git
> >     <http://git.gromacs.org/gromacs.git>".
> >
> >     Did you do git pull?
> >
> >      > From the
> >      > gromacs directory that git created I ran "./bootstrap" and then
> >     ./configure
> >      > .....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
> >     forcefield.
> >      > Finally, when I ran pdb2gmx and chose ffcharmm27 as a forcefield
> >     pdb2gmx
> >      > gave the following error:
> >      >
> >      > Fatal error:
> >      > in .rtp file in residue cmap at line:
> >      >    -C    N    CA    C    +N
> >
> >
> >     /Pär
> >
> >      >>>
> >      >>> 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
>
> --
> ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
>
>
> ------------------------------
>
> Message: 2
> Date: Wed, 13 Jan 2010 10:16:32 +0100
> From: P?r Bjelkmar <bjelkmar at cbr.su.se>
> Subject: [gmx-users] Re: charmm, cmap and gromacs 4.1
> To: gmx-users at gromacs.org
> Message-ID: <4A68E3BB-5A4F-447F-BAA5-ED4CE3B74780 at cbr.su.se>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Hi again,
>
> > 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
> >   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?
>
>
> Hmmm, seems like you have done everything correct. If you have not renamed
> the force filed files the entry in FF.dat should look like this:
> ffcharmm27 CHARMM 27 all-atom force field
> and don't forget to increase the number of the first line in the file
> either!
>
> You could also try to run pdb2gmx with the flag -ff ffcharmm27 and see if
> that works (instead of selecting it interactively from FF.dat). Also take a
> look in the pdb2gmx output and see if any of the ffcharmm27 parameter files
> (I think ffcharmm27.rtp should be the first one read by pdb2gmx) are read.
>
> I did the gromacs installation myself yesterday and I got it to work.
>
> Regards,
> Pär
>
>
Ran everything from the start again and it worked fine. Probably forgot to
do something earlier.
Thank you
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