RE: AMBER: using glycam04 parameters

From: Ross Walker <>
Date: Thu, 19 Apr 2007 12:00:01 -0700

> from another force field. This has to be done with caution. The
> recent versions of Glycam (04-06) was developed using unity scaling
> factors (ie. SCEE=SCNB=1). This is in contrast to how the other
> Amber force fields are developed. Mixing parameters from different
> force fields is likely to introduce artifacts into the calculations,

Is this true? I thought that the Glycam 04 force field - in contrast to the
earlier Glycam versions - specifically used SCEE = 1.2 and SCNB = 2.0 so
that one could mix sugar and amino acid simulations which earlier could not
be done?

Or perhaps I am confusing things here with 10-12 vs 6-12 VDW terms...

Perhaps Rob Woods could comment some more on how one mixes AMBER amino acid
force fields with the Glycam force fields in a single simulation... If the
different value of SCEE in the two force fields is indeed still an issue
then perhaps we should look to implement this "mixture" in the code... -
Perhaps by just hardwiring the prmtop and do away with scee and scnb as
namelist variables all together??

All the best

|\oss Walker

| HPC Consultant and Staff Scientist |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- |
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Received on Sun Apr 22 2007 - 06:07:33 PDT
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