constraint file from amber prmtop/inpcrd

From: amin_at_imtech.res.in
Date: Sat May 24 2014 - 14:32:55 CDT

 

Dear all,

I am trying to run a simulation of a protein in namd using amber ff. For
constraining the protein backbone, I generated a pdb file as follows.
Loaded prmtop file and then inpcrd file.

set all [atomselect top all]

set sel [atomselect top "protein and noh"]

$all set beta 0

$sel set beta 1

$all writepdb protein_cons.pdb

Now when I see this pdb file in vmd by coloring based on beta, it looks
good. But when I use this pdb for fixing or constraining atoms, it
doesn't work and all the atoms keep moving throughout the simulation.
The relevant section of my config file is

fixedAtoms on
fixedAtomsForces on
fixedAtomsFile protein_restrained.pdb
fixedAtomsCol B

constraints on
consRef protein_ca.pdb
consKFile protein_ca.pdb
consKCol B

This method works when i use a psf/pdb file which saves the pdb in a
slightly different format than on using top/crd files. For example

for psf/pdb

CRYST1 0.000 0.000 0.000 90.00 90.00 90.00 P 1 1
ATOM 1 N POPCL 1 -68.750 -75.621 20.887 1.00 1.00 L11 N
ATOM 2 C11 POPCL 1 -68.023 -74.839 22.005 1.00 1.00 L11 C
ATOM 3 C12 POPCL 1 -68.874 -74.862 19.662 1.00 1.00 L11 C
ATOM 4 C13 POPCL 1 -70.159 -76.034 21.305 1.00 1.00 L11 C
ATOM 5 C14 POPCL 1 -68.115 -76.902 20.570 1.00 1.00 L11 C

for top/crd

CRYST1 0.000 0.000 0.000 90.00 90.00 90.00 P 1 1
ATOM 1 N TYR X 1 19.125 9.627 -48.120 0.00 1.00
ATOM 2 H1 TYR X 1 18.710 10.461 -48.511 0.00 0.00
ATOM 3 H2 TYR X 1 19.507 9.072 -48.872 0.00 0.00
ATOM 4 H3 TYR X 1 19.709 9.891 -47.339 0.00 0.00
ATOM 5 CA TYR X 1 18.046 8.808 -47.540 0.00 1.00

Can this be the reason for not getting required constraints? I would be
really thankful for any help.

Regards.

Amin.

 

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