AMBER Archive (2006)

Subject: AMBER: bugfix for impropers in parmchk

From: Kateryna Miroshnychenko (kateryna_mirosh_at_ire.kharkov.ua)
Date: Wed Jan 18 2006 - 08:48:55 CST

Dear all,

As I wrote before, I've found that parmchk treat impropers
incorrectly: in frcmod some impropers were missing, others were
written with central atom standing on the first position instead of
the third one. Since I've received no response neither from the mail
list nor from the author of the program (dr. Wang), I've had to fix
this problem myself :(. Finally I've done this :) and I'm attaching
now the bugfix for parmchk.c. May be it will be helpful to someone
else also.

Best regards,
Katya

> Dear AMBER users,
> I've noticed the strange action of parmchk with improper torsions:
> even for standard residue (RC for example) and ff99 parmchk found
> missing improper parameters, that are listed below
>
> parmchk -i RC.ac -f ac -o RC.frcmod
> -p $AMBERHOME/dat/leap/parm/parm99.dat
>
> (from the frcmod file)
> IMPROPER
> N*-CT-CM-C 1.1 180.0 2.0 Using default value
> CM-N*-H4-CM 1.1 180.0 2.0 Using default value
> CM-CM-HA-CA 1.1 180.0 2.0 Using default value
> CA-CM-N2-NC 1.1 180.0 2.0 Using default value
> C -N*-NC-O 1.1 180.0 2.0 Using default value
>
> It looks like there is a problem with definition of improper torsions
> in parmchk: the first atom should be in the third position (N*-CT-CM-C
> -- CM-C-N*-CT). Any suggestions how to fix this problem would be
> helpful.
>
> With many thanks in advance,
> Katya

********************************************
 Kateryna Miroshnychenko
post-graduate student
Department of Biological Physics,
Institute of Radiophysics and Electronics,
National Academy of Sciences of Ukraine,
12, Proskura st., Kharkiv, 61085, Ukraine
E-mail:kateryna_mirosh_at_ire.kharkov.ua
********************************************

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