Re: topology files

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Thu Sep 24 2009 - 14:16:17 CDT

On Thu, Sep 24, 2009 at 2:17 PM, Sridhar Vaddadi
<Sridhar.Vaddadi_at_utsa.edu> wrote:
> Dear Community,

dear sridhar,

before you keep posting variants of the same question over and over again,
please take the time and go thoroughly over the various tutorials that explain
how to set up simple and not so simple simulations with namd, build topologies
and so on, and also search the mailing list archives. practically everything you
ask about has been answered before and it looks like you are making your
own life needlessly complicated by working out all the details in small steps.

> 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.

from the PDB file format documentation:

The MASTER record is a control record for bookkeeping.

it will be ignored.

the documentation for the PDB file format is available online.
this a simple search in google would have answer your question...

cheers,
    axel.

>
> regards
> Sridhar Vaddadi
> ________________________________
> From: Ramya Gamini [mailto:ramyabhargavi_at_gmail.com]
> Sent: Wed 9/23/2009 5:17 PM
> To: Sridhar Vaddadi
> Cc: namd-l_at_ks.uiuc.edu
> Subject: Re: namd-l: topology files
>
> 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
>

-- 
Dr. Axel Kohlmeyer    akohlmey_at_gmail.com
Institute for Computational Molecular Science
College of Science and Technology
Temple University, Philadelphia PA, USA.

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