Re: topology files

From: Ramya Gamini (ramyabhargavi_at_gmail.com)
Date: Wed Sep 23 2009 - 17:17:28 CDT

Hi Sridhar,

A good site to look into would be
http://www.ks.uiuc.edu/Training/Tutorials/

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.

best
Ramya

On Wed, Sep 23, 2009 at 1:59 PM, Sridhar Vaddadi
<Sridhar.Vaddadi_at_utsa.edu>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 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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