AMBER Archive (2006)

Subject: AMBER: loading torsion parameters

From: Nitin Bhardwaj (nbhardwaj_at_gmail.com)
Date: Mon Jul 31 2006 - 14:47:19 CDT

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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