From: Kenno Vanommeslaeghe (kvanomme_at_rx.umaryland.edu)
Date: Wed Jul 16 2014 - 12:24:29 CDT
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.
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:
Christopher Mayne's advice in this thread is sound.
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