I have had a related problem. The way of having restraints is that you
generate a PDB file with occupancy or beta column marked. For beta
columns the following should work in VMD :
set all [atomselect top all]
set sel [atomselect top "protein"]
$all set beta 0
$sel set beta 1
$all savepdb restrain.pdb
Then in the configuration file for namd you write
fixedAtoms on
fixedAtomsForces on
fixedAtomsFile restrain.pdb
fixedAtomsCol B
or
constraints on
consRef restrain.pdb
consKFile restrain.pdb
consKCol B
The problem I encountered was that this worked when I used a psf/pdb
pair but not when I used a prmtop/inpcrd pair i.e. the atoms kept moving
even after fixing. If you find a solution to this please post on the
list.
Amin.
On 2014-05-30 21:28, Jason Swails wrote:
> On Fri, 2014-05-30 at 11:46 -0400, Lara rajam wrote:
>
>> Dear amber I am trying to use the amber in namd I have already got the links through [ AMBER group]and they are useful I am not understanding the restrain for equilibration in namd ( fixing the solute molecule), How one should do it ?
>
> I believe you need a PDB file for this, and the occupancy column is used
> to mark atoms to restrain, and I _think_ VMD has a utility that will
> create this file for you.
>
>> suggestions regarding this will help me in understanding
>
> This mailing list is probably the wrong place for questions about
> running NAMD (most people here -- and all of the frequent responders --
> use Amber mostly, if not exclusively). You would have better luck
> answering your questions by looking in the NAMD user manual and
> consulting with the NAMD mailing list instead. This task is
> sufficiently common that I would be surprised if their manual did not
> tell you how to do this.
>
> HTH,
> Jason
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Received on Fri May 30 2014 - 10:00:02 PDT
