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On 21/02/2012 12:33 PM, jneeraj wrote:
<blockquote cite="mid:1329788028998-4489663.post@n6.nabble.com"
type="cite">
<pre wrap="">Thank you Mark for you prompt response. I tried:
$pdb2gmx -ignh -merge all -chainsep ter -ff amber99sb -water tip3p -f <pdb>
-o <gro> -p <top>
$grompp -f <mdp> -c <gro> -p <top> -o <tpr>
and it works perfectly, i.e. it correctly creates interchain disulfide bond.
However, when I use charmm27 force field instead of amber99sb, I get the
following error from grompp:
----------------------------------------------------------------------------
Program grompp, VERSION 4.5.5
Source code file: toppush.c, line: 1346
Fatal error:
Unknown cmap torsion between atoms 3224 3226 3228 3234 3237
----------------------------------------------------------------------------
So I believe this error is specific to charmm27 force-field. Any thoughts ?
</pre>
</blockquote>
<br>
Because those are the atoms across the 1-C 2-N region, that suggests
that the mechanism that adds CMAP to the backbone is not interacting
correctly with the -merge mechanism. Please open a new issue on
Redmine <a href="http://redmine.gromacs.org/">http://redmine.gromacs.org</a>
and attach files that will reproduce the problem. If my guess is
correct, the fix should be straightforward.<br>
<br>
Mark<br>
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