AMBER Archive (2006)

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

From: Ross Walker (
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

|\oss Walker

| HPC Consultant and Staff Scientist |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- |
| | PGP Key available on request |

Note: Electronic Mail is not secure, has no guarantee of delivery, may not
be read every day, and should not be used for urgent or sensitive issues.

The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to