From: Ross Walker <>
Date: Wed, 24 Mar 2010 16:00:55 -0700

Hi Lekpa,

> I need some advice regarding FF parameters.
> I have a molecule where a covalent bond exists between a peptiod and a
> sugar. Parameters exist in AMBER and GLYCAM respectively for each but
> due to
> scaling (dihedral rotamer population is important in my work)issue with
> SCEE and SCNB I have derived charges for the peptiod using the GLYCAM
> approach ( ~200 structures from MD, CHelpG, 0.01 wt etc ). This is
> relatively easy as my system is small. MD using the new charges (
> without
> SCEE/SCNB scaling of course and using AMBER valence parameters ) yield
> very
> similar structures (rsmd) in solution as model using parm99SB charges.
> I am thinking this is probably fine but I would like people's opinion!

This seems reasonable 'except' that the parameters in AMBER, specifically
the dihedral terms assume default SCEE=1.2 and SCNB=2.0. Thus you would have
to re-parameterize the dihedrals as well. You should note that AMBER 11 (to
be released in a few weeks) will address this issue allowing variable 1-4
scaling to be done. AMBER 10 supports this in PMEMD (NOT sander) after
applying bugfix.26. Thus you may want to wait until AMBER 11 or if you want
to use AMBER 10 email me off list and I'll explain how to setup the relevant
sections of the prmtop that you will need. This will let you use the
standard charge and dihedral parameters for both GLYCAM and FF99SB together.
You will still need to provide covalent parameters for the FF99SB to GLYCAM
bond, angle and dihedrals.

All the best

|\oss Walker

| Assistant Research Professor |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- |
| | |

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Received on Wed Mar 24 2010 - 16:30:02 PDT
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