AMBER Archive (2007)

Subject: Re: AMBER: bugfix for impropers in parmchk

From: Jiten (jiten_at_postech.ac.kr)
Date: Wed Aug 01 2007 - 23:02:24 CDT

I just wonder if this problem is completely resloved as I could not see the
relevent bug-fixes in the amber8 bug fixed list.

Thanks for any response.

JITEN
----- Original Message -----
From: "Kateryna Miroshnychenko" <kateryna_mirosh_at_ire.kharkov.ua>
To: <amber_at_scripps.edu>
Sent: Wednesday, January 18, 2006 11:48 PM
Subject: AMBER: bugfix for impropers in parmchk

> 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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