AMBER Archive (2006)

Subject: RE: AMBER: organic molecule - from newbie :)

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Mon Apr 10 2006 - 17:41:56 CDT

> Now that I have my parm file for my organic molecule (having
> followed Ross
> Walker's tutorial 5 step by step) I still have a couple of
> questions :)
>
> 1) I see that my frcmod is empty. Is that b/c all of the
> required info are
> in the prmtop file?

Yes, in this case you should be good to go. If the prmtop file was created
then all is good.
 
> 2) How can I add polarizability to my molecule?

This is a difficult one. The Gaff forcefield was not designed for
polarisable simulations and so no parameters are available (as far as I
know). Thus to do a polarisable simulation you would need to use the FF02
forcefield and develop the parameters for your molecule inline with this. Do
you definately need to use a polarisable force field? Alternatively if you
just want polarisability for the active site you could try a QM/MM approach
but you should probably stick to regular simulations to begin with so you
can validate your approach.

All the best
Ross

/\
\/
|\oss Walker

| HPC Consultant and Staff Scientist |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- ross_at_rosswalker.co.uk |
| http://www.rosswalker.co.uk | PGP Key available on request |

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