AMBER Archive (2004)

Subject: Re: AMBER: problems with dihedrals - extended information

From: David A. Case (case_at_scripps.edu)
Date: Mon Oct 18 2004 - 12:42:50 CDT

On Sun, Oct 17, 2004, Petr Kulhanek wrote:

>
> in parm A, the dihedrals of type H1-CT-CT-OH have assigned following
> parameters
> PK PN PHASE
> 0.25000 1.0 0.0
>
> in parm B, the dihedrals of type H1-CT-CT-OH have assigned following
> parameters
> PK PN PHASE
> 0.25000 1.0 0.0
> 0.15556 3.0 0.0
>
> in parm A, the dihedral of type OH-CT-CT-OH has assigned following
> parameters
> PK PN PHASE
> -0.67000 1.0 0.0
> 0.500000 2.0 0.0
>
> in parm B, the dihedral of type OH-CT-CT-OH has assigned following
> parameters
> PK PN PHASE
> -0.67 1.0 0.0
> 0.5 2.0 0.0
> 0.15556 3.0 0.0
>
> Above mentioned dihedral types match following parameters from both
> parm99.dat and glycam_2000a.dat files.
> (parm99.dat)
> X -CT-CT-X 9 1.40 0.0 3.
> H1-CT-CT-OH 1 0.25 0.0 1.
> OH-CT-CT-OH 1 0.144 0.0 -3.
> OH-CT-CT-OH 1 1.175 0.0 2.
>
> (glycam_2000a.dat)
> X -CT-CT-X 9 1.40 0.00 3.
> OH-CT-CT-OH 1 -0.67 0.00 -1.
> 1 0.50 0.00 2.
>

Thanks for the detailed analysis. It looks like something funny is going on
when a second parameter file (in this case glycam_200a) is read in that
changes the definitions of a previous one (in this case par99). Especially(?)
when the number of terms for a given dihedral angle is different in the two
files.

Ultimately, there probably needs to be a code fix, but in your case you need
to figure out which OH-CT-CT-OH and H1-CT-CT-OH parameters you want: the ones
in glycam2004 or in parm99). Then you could remove the ones you don't want,
and see if that helps.

I don't yet see, though, why you are getting different results for the ligand
and for the complex.

...regards....dac

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