AMBER Archive (2006)

Subject: Re: AMBER: loading torsion parameters

From: Wei Zhang (zweig_at_scripps.edu)
Date: Mon Jul 31 2006 - 15:13:57 CDT

Dear Nitin,

  I think somebody has experienced your problems before. It seems xleap
has very restrict requirements on dihedral parameters. My suggestion is
copy a line from parm99.dat 's dihedral parameter section, change it into
you parameter, do not delete any space or tab from the original line, it
might will solve your problem.

  Sincerely,

  Wei

Nitin Bhardwaj wrote:

> Dear amber users,
> I have 4 cystines coordinating 1 zinc atom in my protein. So, I
> changed the CYS to CYM and then created a bond between the sulphur
> atoms of CYM using the 'bond' command. For the new 4 bonds created, i
> took the parameters from Ross walker's thesis and created a frcmod
> file which looks like this:
>
> BOND
> SH-ZNA 81.7 2.293
> NB-ZNA 85.5 2.101
> ....
>
> ANGLE
> SH-ZNA-SH 49.5 146.5
> NB-ZNA-SH 30.4 103.0
> .....
>
> DIHE
> CC-NB-ZNA-SH -2.82 0.00 2.0
> CR-NB-ZNA-SH -2.82 0.00 2.0
> SH-ZNA-SH-CT -0.03 0.00 2.0
> .....
>
> Before i loaded this file, when i said 'check unit', it gave some
> errors like:
> Could not find bond parameter for: NB - ZNA
> No bond parameter for: NB - ZNA
> Could not find bond parameter for: SH - ZNA
> No bond parameter for: SH - ZNA
> Could not find bond parameter for: SH - ZNA
> No bond parameter for: SH - ZNA
> Could not find bond parameter for: SH - ZNA
> No bond parameter for: SH - ZNA
> Checking for angle parameters.
> Could not find angle parameter: CR - NB - ZNA
> Can't find angle parameter: CR - NB - ZNA
> Could not find angle parameter: NB - ZNA - SH
> Can't find angle parameter: NB - ZNA - SH
>
> Of course these diappeared after i loaded the frcmod file with the
> parameters.
> But when I say
> saveamberparm t t.prmtop t.inpcrd
> it gives me the error:
> Building proper torsion parameters.
> ** No torsion terms for CR-NB-ZNA-SH
> ** No torsion terms for CR-NB-ZNA-SH
> ** No torsion terms for CR-NB-ZNA-SH
> ** No torsion terms for NB-ZNA-SH-CT
> ** No torsion terms for NB-ZNA-SH-CT
> ** No torsion terms for NB-ZNA-SH-CT
> ** No torsion terms for CC-NB-ZNA-SH
> ** No torsion terms for CC-NB-ZNA-SH
> ** No torsion terms for CC-NB-ZNA-SH
> ** No torsion terms for SH-ZNA-SH-CT
>
> Although I have these parameters in my frcmod file. Why is Xleap not
> reading the dihedral parameters from the frcmod file but is reading
> the bind and angle terms.
> Is there another way to load the torsion parameters? Is there
> something worong with my parameters format?
>
> thank a lot in anticipation.
> Rgds
> Nitin
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