From: Aron Broom (broomsday_at_gmail.com)
Date: Tue Jul 15 2014 - 21:58:07 CDT
it might be helpful to get a sense of the general flow one goes through
when parameterizing something. In the simplest case it would look like:
1) get the partial charges for your atoms based on at least one structure
(you can use more than one to get a more accurate derivation, but might be
simplest to stick with one). I'm not sure if CGenFF or any of the VMD
tools allow for this, but I do know the RESP server
http://q4md-forcefieldtools.org/REDS/ is designed for this.
2) find a forcefield which has some general atom types such that it can
handle all the bond, angle, and dihedral terms. I think there is such a
thing for CHARMM, others on the list would have a better sense, but at
least there is also the general amber forcefield. Then you either look at
the atom types in some documentation of the forcefield, and assign yours
based on their bonding/chemical environment, or perhaps let some automated
script attempt this (I've only ever done it manually).
3) now you have a molecule that has bond, angle, and dihedral terms, and
you add in (or it might get automatically done depending on the tools you
are using) your partial charges, and viola! You have a classical
CHARMM-like forcefield parameter for your molecule.
I don't know much about the outputs you mentioned, but typically, I think a
.mol2 file is meant to be a simple format that nontheless contains at least
the partial charge information, if not also something about bonding (things
that are not in a typical PDB).
Certainly the website of the server I mentioned has some tutorials on this
process. Good luck!
On Tue, Jul 15, 2014 at 12:55 PM, Abhishek TYAGI <atyagiaa_at_connect.ust.hk>
> I want to run MD, but unfortunately I do not have the reasonable force
> field for this molecule.
> Now what I tried following approaches to get force field:
> 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.
> 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?
> 3. I tried parameter tool available in VMD too I got some output from it
> too, but I am not able to connect all the information.
> Any guess what to do to get accurate force field parameter for the molecule
-- Aron Broom M.Sc PhD Student Department of Chemistry University of Waterloo
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