[gmx-users] unknown cmap torsion between atoms

[Justin A. Lemkul]

On 5/25/12 5:04 PM, Steven Neumann wrote:
>
>
> On Fri, May 25, 2012 at 2:34 PM, Justin A. Lemkul <jalemkul at vt.edu
> <mailto:jalemkul at vt.edu>> wrote:
>
>
>
>     On 5/25/12 5:52 AM, Steven Neumann wrote:
>
>         Dear Gmx Users,
>
>         My system is made of 3 proteins. As I want to use distance restraints
>         dynamics
>         between atoms belonging to each of them I have to produce topoloy with one
>         moleculetype. I used pdb2gmx -chainsep interactive (I used merge: yes).
>
>         Then when I process to grompp the error: "unknown cmap torsion between atoms
>         ......."
>
>         These atoms belong to the last residue of the chain A and to the first
>         residue
>         of Chain B. How to get rid of this? Please, help.
>
>
>     http://redmine.gromacs.org/__issues/885 <http://redmine.gromacs.org/issues/885>
>
>     Either apply Mark's patch posted there or download the latest
>     release-4-5-patches branch via git.
>
>     -Justin
>
>
> Thanks! I need to talk to the administrator as the Gromacs I am using is on the
> cluster. Would you suggest to install GMX 4.5.5 first and then apply the patch?
>

It is generally best to work with the latest version unless you have some reason 
(like scientific continuity) to use an old version, especially when applying 
patches and bug fixes.  You can always install within your own home directory if 
you don't want to wait on an admin to install a (technically) non-standard 
Gromacs version system-wide.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
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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