From: Abhishek TYAGI (atyagiaa_at_connect.ust.hk)
Date: Sat Jul 19 2014 - 07:44:53 CDT
Dear Kenno,
Thankyou for the suggestion, I had read all the information provided so far and gone through the links in detail. But still I have a silly question, right now I have a.mol2 file and I got CGenFF a.str file, and for psfgen If I use a.str file it shows error, therefore I used CHARM-GUI to get psf and pdb file, I tried doe quick md on C-GUI it gives some topology and prm file, I used them for my simulation and got error, and for other files top and prm I still confused how to proceed.
regards
Abhi
________________________________________
From: owner-namd-l_at_ks.uiuc.edu <owner-namd-l_at_ks.uiuc.edu> on behalf of Kenno Vanommeslaeghe <kvanomme_at_rx.umaryland.edu>
Sent: Thursday, July 17, 2014 1:24 AM
To: namd-l_at_ks.uiuc.edu
Subject: Re: namd-l: Force field design
On 07/15/2014 12:55 PM, Abhishek TYAGI wrote:
> 1. I tried CGenFF and got a *.str file but the data in the file is different from my input file i.e. mol2 file, the pdb format is different from the *.str file.
The str file contains a force field for your molecule, while the mol2 and
pdb formats contain a geometry. How could the data not be different???
The str file is a concatenated topology and parameter file. NAMD knows to
ignore the topology section and can read the file as it is.
http://mackerell.umaryland.edu/~kenno/cgenff/program.html#namd
I believe psfgen does the same (read the topology and ignore the
parameters) though I'm less sure about that.
> 2. I tried to get force field from swissparam website and received the different file as *.par, *.top file, I tried MD on this field it runs successful, but the question is that is this correct approach?
It is strongly encouraged to search the archive before posting a question.
If you had, you would have discovered the use of SwissParam for
condensed-phase calculations is discouraged, and found advise on better
ways to do it:
http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l.2013-2014/0846.html
http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l.2013-2014/0893.html
http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l.2013-2014/1250.html
Christopher Mayne's advice in this thread is sound.
This archive was generated by hypermail 2.1.6 : Wed Dec 31 2014 - 23:22:37 CST