psfgen

From: Sridhar Vaddadi (Sridhar.Vaddadi_at_utsa.edu)
Date: Wed Sep 23 2009 - 17:11:37 CDT

Dear Community
I am doing a NAMD calculation. I have an XYZ file of HISTIDINE-ARGININE DI PEPTIDE STRUCTURE. After generating pdb file from this XYZ, during psf generation using VMD after giving topology file name, Is it necessary to give alias residue and ailas atom because I tried both with alias and without alias and I am ending up with fatal error msg. Please help in this regard.
Cheers,
Sridhar Vaddadi

________________________________

From: owner-namd-l_at_ks.uiuc.edu on behalf of Sridhar Vaddadi
Sent: Wed 9/23/2009 1:59 PM
To: namd-l_at_ks.uiuc.edu
Cc: alex_at_outerbanks.umaryland.edu
Subject: namd-l: topology files

 
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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