AMBER Archive (2006)

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

From: Raffaella D'Auria (rdauria_at_uci.edu)
Date: Mon Apr 10 2006 - 17:12:44 CDT

Dear All,

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?

2) How can I add polarizability to my molecule?

Thanks a lot!

Raffaella.

On Thu, 6 Apr 2006, Ross Walker wrote:

> Dear Raffaella,
>
> > I would like to simulate an organic molecule (an alcohol) in water. I
> > have been reading the manual (amber 8) to understand how to build the
> > force field for a simple alcohol (or to use what is already in the
> > distribution). However I am not getting very far in
> > understanding how to
> > do it (meaning how to build the residue and the parameter file).
>
> I would try taking a look at the tutorials at:
>
> http://www.rosswalker.co.uk/tutorials/amber_workshop/
>
> Particularly tutorials 4 and 5.
>
> These will take you through step by step creating prmtop files for
> non-standard residues and will show you both the manual and antechamber
> approaches...
>
> 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 |
>
> 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 amber_at_scripps.edu
> To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu
>

____________________________________________________________________
Raffaella D'Auria, PhD | e_mail: rdauria_at_uci.edu
Department of Chemistry |
3218 Natural Sciences 1 | ph. n.: 949-824-9921
University of California, Irvine |
____________________________________________________________________
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu