Re: fixed residue

From: Roman Petrenko (rpetrenko_at_gmail.com)
Date: Mon Jul 28 2008 - 23:36:45 CDT

suppose you want to fix CA atom of residue number 2. in your input
file myfile.pdb file you have a line

ATOM 25 CA GLY A 2 -0.164 2.464 -3.421 1.00 0.00 C

change it to
ATOM 25 CA GLY A 2 -0.164 2.464 -3.421 1.00 1.00 C

and save as myfile_fixed.pdb

then add the following three lines to namd config file (anywhere
before "run" statement)

fixedAtoms on
fixedAtomsFile myfile_fixed.pdb
fixedAtomsCol B

On Mon, Jul 28, 2008 at 11:49 PM, Rudra Banerjee <bnrj.rudra_at_yahoo.com> 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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-- 
Roman Petrenko.
Physics Department
University of Cincinnati

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