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)
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!
> 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
> JRF; SNBNCBS
> A bus station is where a bus stops. A train station is where a train
> stops. On my desk I have a work station.
> Please, if possible, don't send me MS Word or PowerPoint attachments
> Why?See: http://www.gnu.org/philosophy/no-word-attachments.html
> Unlimited freedom, unlimited storage. Get it now, on http://help.yahoo.com/l/in/yahoo/mail/yahoomail/tools/tools-08.html/
-- Roman Petrenko. Physics Department University of Cincinnati
This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:49:41 CST