AMBER Archive (2003)

Subject: Re: parm99

From: David A. Case (case_at_scripps.edu)
Date: Tue May 20 2003 - 17:37:32 CDT

On Tue, May 20, 2003, cailliez wrote:

> There is still something I do not understand with parm99. In parm99.dat,
> there are lots of new parameters, including some new parameters for tyrosine
> concerning valence angles or torsionnal angles. Reading parm99.dat, I
> understand that these changes for tyrosine must be done by changing the type
> of CZ atom from C (in parm98) to CA (in parm99).

This looks like a bug to me: there doesn't seem to be any easy way to
use the parm99 tyrosine parameters for non-polarizable simulations, since
all_amino94.in still has the old atom types. [The polarizable libraries,
like all_amino02.in and all_amino02EP.in *do* have this change.]

Junmei: do you have a recommended solution for this?

The only workaround I see is to manually modify the TYR unit to change the
atom type of CZ, before loading in your pdb file.

Thanks for the report ... we'll try to figure out the best fix (so as not
to break older simulations that use ff94). This change is probably pretty
minor, but definitely looks to me like it is wrong.

..regards...dac 

-- 

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David A. Case                     |  e-mail:      case_at_scripps.edu
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