[AMBER] Namdenergy problems with non-standard amino acids

From: Clavel <dclavel.ibs.fr>
Date: Thu, 09 Jul 2015 11:34:53 +0200

Hello everyone,

I am currently computing van der Waals interaction energy within a large
set of residues from a MD simulation.
I wrote a script for computing the vdW interaction energies by using the
namdenergy plugin that is looking like:

> package require namdenergy
> set res58 [atomselect top "protein resid 58"]
> set res61 [atomselect top "protein resid 61"]
> set output [open 2_A.dat w]
> set nf [molinfo top get numframes]
> set namdvdw [ namdenergy -vdw -sel $res58 $res61 -cutoff 12
-ofile 2_A.dat]]
> puts $output " sim #: _A "
> close $output
> $res58 delete
> $res61 delete

However, $res61 is a non standard amino acid. I have done my MD
simulation with a specific force field for such residue.

I would like to know how to use namdenergy plugin with a specific force
field because so far the plugin is not able to compute the vdW
interaction energy with my script.


*Damien CLAVEL*
Cellphone +33 7 81 66 61 70
Landline   +33 4 57 42 87 35
PhD student at Laboratoire Chimie Physique (UP Sud)
                 and Institut de Biologie Structurale (EPN Campus)
Laboratoire de Chimie Physique 
<http://www.lcp.u-psud.fr/rubrique.php3?id_rubrique=266/> Institut de 
Biologie Structurale <http://www.ibs.fr/spip.php?lang=en>
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Received on Thu Jul 09 2015 - 03:00:02 PDT
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