> Message: 1 > Date: Tue, 12 Jan 2010 19:13:20 -0500 > From: "Justin A. Lemkul" <[email protected]> > Subject: Re: [gmx-users] Re: charmm, cmap and gromacs 4.1 > To: Discussion list for GROMACS users <[email protected]> > Message-ID: <[email protected]> > 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 <[email protected]> > Subject: [gmx-users] Re: charmm, cmap and gromacs 4.1 > To: [email protected] > Message-ID: <[email protected]> > 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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