topology files

From: Sridhar Vaddadi (Sridhar.Vaddadi_at_utsa.edu)
Date: Wed Sep 23 2009 - 13:59:02 CDT

 
Dear Community,
I am new to NAMD. I am trying to run NAMD on HIS-ARG dipeptide. When I am trying to generate psf file, it is asking for topology file. I downloaded topology files from http://mackerell.umaryland.edu/CHARMM_ff_params.html. In this webpage I found,
 

Toppar files with c35b2, c36a2 release of CHARMM.

toppar_c35b2_c36a2.tgz

what does c35b2 and c36a2 indicate and how do I choose what file I required for my calculation.

Any suggestions are really appreciated.

regards

Sridhar Vaddadi
 

________________________________

From: owner-namd-l_at_ks.uiuc.edu on behalf of Sridhar Vaddadi
Sent: Wed 9/23/2009 11:23 AM
To: namd-l_at_ks.uiuc.edu
Subject: namd-l: help requested

Dear Community,
 
I am planning to run a NAMD simulation on HIS-ARG peptide. I have XYZ coordinates of this system. Can any one suggest how to generate pdb and psf files from this XYZ system. Is, VMD a good help to do this. Your suggestions are really appreciated.
 
regards
Sridhar Vaddadi

________________________________

From: owner-namd-l_at_ks.uiuc.edu on behalf of Rick Calloway
Sent: Tue 9/22/2009 12:08 PM
To: namd-l_at_ks.uiuc.edu
Subject: namd-l: Precision of Coordinate data

Hi community,
 
Can someone help me better understand the precision of the output coordinate data.
 
I am looking for statistically significant movement of the center of mass of a large molecule. Using VMD's measure center command returns angstroms out to 15 decimal places and looks quite tempting.
 
If the last 12 or so decimal places had meaning I could significantly reduce the runtime for my system.
 
How can I determine how many of these digits are significant?
 
Thank you in advance.
 
Rick Calloway

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