RE: topology files

From: Sridhar Vaddadi (
Date: Thu Sep 24 2009 - 13:17:26 CDT

Dear Community,
Can anyone explain the importance of MASTER line at the end of the pdb file. It has a series of numbers and I want to know what they infer for and how important for psfgen.
Sridhar Vaddadi


From: Ramya Gamini []
Sent: Wed 9/23/2009 5:17 PM
To: Sridhar Vaddadi
Subject: Re: namd-l: topology files

Hi Sridhar,

A good site to look into would be

You will find simple tutorials to get you started with NAMD. Also, you will find the required topology and parameter files for protein systems in any of the tutorial files that come along with the tutorials.


On Wed, Sep 23, 2009 at 1:59 PM, Sridhar Vaddadi <> wrote:

        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 In this webpage I found,

        Toppar files with c35b2, c36a2 release of CHARMM.


        toppar_c35b2_c36a2.tgz <http://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.


        Sridhar Vaddadi


        From: on behalf of Sridhar Vaddadi
        Sent: Wed 9/23/2009 11:23 AM
        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.
        Sridhar Vaddadi


        From: on behalf of Rick Calloway
        Sent: Tue 9/22/2009 12:08 PM
        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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