AMBER Archive (2009)

Subject: RE: [AMBER] Possibility to use ff99 + GAFF + GLYCAM_06 in one time for complex system ?

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Tue Apr 14 2009 - 18:27:37 CDT

Hi Marek,

> thank you very much for your complex and valuable answer !
>
> Just for the curiosity, is this discussed combination:
>
> GLYCAM_06 + ff99SB + GAFF
>
> remarkably better solution than only:
>
> ff99SB + GAFF
>
> ?

I would be VERY surprised if GAFF gets the subtleties of conformation in
sugars correct. To the point that I think the error would be larger than the
1-4 scaling not necessarily being optimal. This is only a hunch though, I
have not tried it. Your best option would probably be to try a single
maltose and let Antechamber parameterise it and then compare certain
properties (dihedral barriers etc) with the Glycam 06 ones. This will give
you an idea of the differences.

Rob Woods can probably comment some more on this.

All the best
Ross

/\
\/
|\oss Walker

| Assistant Research Professor |
| 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.

_______________________________________________
AMBER mailing list
AMBER_at_ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber