AMBER Archive (2006)

Subject: Re: AMBER: bugfix for impropers in parmchk

From: David Mobley (dmobley_at_gmail.com)
Date: Fri Jan 20 2006 - 12:21:49 CST

Katya,

What in particular do you think the bug was? I've noticed the problem
before, but it wasn't clear in what circumstances the bug would pop up, etc.
I've been using parmchk a lot, but because of my awareness of the problem
I've always been manually checking the impropers to make sure they make
sense, so I'm very interested in knowing whether this is actually
definitively resolved.

Thanks,
David

On 1/18/06, Kateryna Miroshnychenko <kateryna_mirosh_at_ire.kharkov.ua> wrote:
>
> 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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