From: Josh Vermaas (vermaas2_at_illinois.edu)
Date: Wed Jul 22 2015 - 08:59:48 CDT
Hi Urszula,
I usually prepare this with a simple vmd script that loads in the
starting pdb and "tags" the atoms I want in the beta column of the
output pdb. This is what you then feed into NAMD using the appropriate
arguments (check the user guide).
mol new initial.pdb
set all [atomselect top "all"]
set sel [atomselect top "noh and backbone"]
$all set beta 0
$sel set beta 1
$all writepdb restrained.pdb
Note that the restraint pdb needs to have all the atoms listed,
regardless of if they are constrained/restrained or not, since that is
what NAMD's parser expects.
-Josh Vermaas
On 07/22/2015 02:59 AM, Urszula Uciechowska wrote:
> Dear all,
>
> I trying to apply the harmonic constraint on my backbone atoms (CA, N, C,
> O). How should I prepare the constraint file? What should be there?
> I created the file with those atoms but after running namd I got an error
> message:
>
>
> Infiniband support is active.
> Namd ibverbs will be loaded by 'apps/namd/2.9'.
> 'compilers/gcc/4.8.0' load complete.
> 'tools/openmpi/1.6.5-gnu-4.8.0-ib' load complete.
> 'apps/namd/2.9' load complete.
> 'tools/scratch/1.0' load complete.
> Charmrun> started all node programs in 1.267 seconds.
> ------------- Processor 0 Exiting: Called CmiAbort ------------
> Reason: FATAL ERROR: Number of atoms in constraint constant PDB doesn't
> match coordinate PDB
>
> Fatal error on PE 0> FATAL ERROR: Number of atoms in constraint constant
> PDB doesn't match coordinate PDB
>
> mpiexec: killing job...
>
> best regards
> Urszula
>
>
>
> University of Gdansk and Medical Univesity of Gdansk
> Department of Molecular and Cellular Biology
> ul. Kladki 24
> 80-822 Gdansk
> Poland
>
>
> -----------------------------------------
> Ta wiadomość została wysłana z serwera Uniwersytetu Gdańskiego
> http://www.ug.edu.pl/
>
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