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

[Justin A. Lemkul]

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

-- 
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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

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