Re: fixed residue

From: Gianluca Interlandi (gianluca_at_u.washington.edu)
Date: Tue Jul 29 2008 - 01:03:40 CDT

You need to have a pdb file where you set the "beta" value of the atoms
you want to be fixed to 1. To do this open your pdb with vmd, e.g.

vmd myprotein.pdb

Open Extensions -> Tk console and type:

[atomselect top all] set beta 0
[atomselect top "resname GLU"] set beta 1
[atomselect top all] writepdb myprotein_fix.pdb

In your config file add the lines:

#fixed atoms
fixedAtoms on
fixedAtomsFile myprotein_fix.pdb
fixedAtomsCol B

Also, have a look at the documentation:

http://www.ks.uiuc.edu/Research/namd/2.6/ug/node28.html#SECTION00091200000000000000

This was short but I hope it helps,

Gianluca

On Tue, 29 Jul 2008, Rudra Banerjee wrote:

> As a beginner with NAMD, i am puzzelesd over how i can fix the atom position!
> i
> have Glu residue solvated in water. Now i want glutamines to be fixed.
> so if i use fixedAtoms tag on, what should i put in the
> fixedAtomfiles? the PDB file name of the gultamine?
> plz help
>
>
> --
> Rudra
> JRF; SNBNCBS
> http://www.bose.res.in/~rudra
>
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-----------------------------------------------------
Gianluca Interlandi, PhD gianluca_at_u.washington.edu
                     +1 (206) 685 4435
                     +1 (206) 714 4303
                     http://biocroma.unizh.ch/gianluca/

Postdoc at the Department of Bioengineering
at the University of Washington, Seattle WA U.S.A.
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