<br><div class="gmail_quote"><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Message: 1<br>
Date: Tue, 12 Jan 2010 19:13:20 -0500<br>
From: "Justin A. Lemkul" <<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>><br>
Subject: Re: [gmx-users] Re: charmm, cmap and gromacs 4.1<br>
To: Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>
Message-ID: <<a href="mailto:4B4D1020.3060801@vt.edu">4B4D1020.3060801@vt.edu</a>><br>
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<br>
<br>
<br>
stefhoor wrote:<br>
> Hi,<br>
><br>
><br>
> > Hello. Thank you for the git repository tip, but I don't think it<br>
> worked<br>
> > out.<br>
> > I tried using "git clone git://<a href="http://git.gromacs.org/gromacs.git" target="_blank">git.gromacs.org/gromacs.git</a><br>
> <<a href="http://git.gromacs.org/gromacs.git" target="_blank">http://git.gromacs.org/gromacs.git</a>>".<br>
><br>
> Did you do git pull?<br>
><br>
> > From the<br>
> > gromacs directory that git created I ran "./bootstrap" and then<br>
> ./configure<br>
> > .....etc.<br>
><br>
> > I inserted the ffcharmm files into the ~GROMACSPATH/top directory<br>
> and edited<br>
> > the FF.dat file to include a eleventh line with the ffcharmm27<br>
> forcefield.<br>
> > Finally, when I ran pdb2gmx and chose ffcharmm27 as a forcefield<br>
> pdb2gmx<br>
> > gave the following error:<br>
> ><br>
> > Fatal error:<br>
> > in .rtp file in residue cmap at line:<br>
> > -C N CA C +N<br>
><br>
><br>
> /Pär<br>
><br>
> >>><br>
> >>> I wanted to use charmm forcefield on gromacs (am using 4.07)<br>
> but when I<br>
> >> try<br>
> >>> using this forcefield gromacs tells me that there is a problem<br>
> with CMAP.<br>
> >> I<br>
> >>> read that gromacs 4.1 is coming with charmm forcefield as well.<br>
> If that<br>
> >> is<br>
> >>> true, when is gromacs 4.1 coming and how can I use charmm FF<br>
> with gromacs<br>
> >>> for now?<br>
> >> The code supporting CHARMM is in git master (see<br>
> >> <a href="http://www.gromacs.org/Developer_Zone/Git/Git_Tutorial" target="_blank">http://www.gromacs.org/Developer_Zone/Git/Git_Tutorial</a>) and<br>
> will, as you<br>
> >> say, be included in version 4.1. Download CHARMM force filed<br>
> files v1.1 from<br>
> >> <a href="http://www.dbb.su.se/user:bjelkmar/ffcharmm" target="_blank">http://www.dbb.su.se/user:bjelkmar/ffcharmm</a>. They will, of<br>
> course, also be<br>
> >> included with 4.1.<br>
> >><br>
> >> Actually, I got the notification yesterday that a paper<br>
> describing this<br>
> >> implementation will be published in JCTC.<br>
> >><br>
> >>> Would it be better to wait for gromacs 4.1?<br>
> >> There might be some minor changes until 4.1 but the current<br>
> (CHARMM-) code<br>
> >> (in git master) is tested and is working well. Once version 4.1<br>
> is released<br>
> >> I would recommend you to update to that version.<br>
> >><br>
><br>
><br>
> Yes, I did git pull and the output is this:<br>
><br>
> remote: Counting objects: 9, done.<br>
> remote: Compressing objects: 100% (5/5), done.<br>
> remote: Total 5 (delta 4), reused 0 (delta 0)<br>
> Unpacking objects: 100% (5/5), done.<br>
> >From git://<a href="http://git.gromacs.org/gromacs" target="_blank">git.gromacs.org/gromacs</a> <<a href="http://git.gromacs.org/gromacs" target="_blank">http://git.gromacs.org/gromacs</a>><br>
> c358dce..b493dbb master -> origin/master<br>
> Already up-to-date.<br>
><br>
> Still charmm does not work. Is there something wrong about the way I<br>
> included the forcefield files in the top directory, should I have<br>
> changed something else?<br>
><br>
><br>
<br>
Have you used the right executable? For instance, where did you install the git<br>
version of Gromacs? Are you using instead another version? I tested the git<br>
version today with CMAP support and it worked fine.<br>
<br>
-Justin<br>
<br>
--<br>
========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | (540) 231-9080<br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
<br>
========================================<br>
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<br>
Message: 2<br>
Date: Wed, 13 Jan 2010 10:16:32 +0100<br>
From: P?r Bjelkmar <<a href="mailto:bjelkmar@cbr.su.se">bjelkmar@cbr.su.se</a>><br>
Subject: [gmx-users] Re: charmm, cmap and gromacs 4.1<br>
To: <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
Message-ID: <<a href="mailto:4A68E3BB-5A4F-447F-BAA5-ED4CE3B74780@cbr.su.se">4A68E3BB-5A4F-447F-BAA5-ED4CE3B74780@cbr.su.se</a>><br>
Content-Type: text/plain; charset="iso-8859-1"<br>
<br>
Hi again,<br>
<br>
> Yes, I did git pull and the output is this:<br>
><br>
> remote: Counting objects: 9, done.<br>
> remote: Compressing objects: 100% (5/5), done.<br>
> remote: Total 5 (delta 4), reused 0 (delta 0)<br>
> Unpacking objects: 100% (5/5), done.<br>
>> From git://<a href="http://git.gromacs.org/gromacs" target="_blank">git.gromacs.org/gromacs</a><br>
> c358dce..b493dbb master -> origin/master<br>
> Already up-to-date.<br>
><br>
> Still charmm does not work. Is there something wrong about the way I<br>
> included the forcefield files in the top directory, should I have changed<br>
> something else?<br>
<br>
<br>
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:<br>
ffcharmm27 CHARMM 27 all-atom force field<br>
and don't forget to increase the number of the first line in the file either!<br>
<br>
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.<br>
<br>
I did the gromacs installation myself yesterday and I got it to work.<br>
<br>
Regards,<br>
Pär<br>
<font color="#888888"><br>
</font></blockquote></div><br>Ran everything from the start again and it worked fine. Probably forgot to do something earlier.<br>Thank you<br><br>
<br><br><br><br><br><br><br><br>