AMBER Archive (2008)

Subject: Re: AMBER: disulfide bridge with ff03ua FF

From: Marcin Krol (krol01_at_cancer.org.uk)
Date: Mon Feb 11 2008 - 09:01:30 CST

Hi

Still can't make a disulfide bridge in ff03ua. leaprc.ff03ua is somewhat
inconsistent - it loads uni_amino03.lib where no CYX is defined, but
then in addPdbResMap it specifies CYX. Since CYX is not defined in
uni_amino03.lib in the first place, leap complains about unrecognized
residue name.
Otherwise, if I read in PDB file with CYS and use command bond
complex.77.SG complex.105.SG it complains about missing parameters for
SH-SH bond, etc. This is correct, because none of parm files has
parametres for SH-SH bond (SH atom type is used in CYS). It has
parameters for S-S bond, but S atom type is used in CYX.
So, it looks like there is a missing CYX residue in uni_amino03.lib. Was
it left out on purpose (eg. one can't have disulfides in ff03ua), or by
mistake?

Any comments will be helpful
m

> Hello Amber Users,
> Sir,
> Thanking You,
> Which vertion you are using in amber ? if
> it is Amber9, then i will send you some thing about making a disulfide
> bridge between CysS-SCys.... 

-- 
Dr Marcin Krol
Biomolecular Modelling Laboratory
Cancer Research UK
London Research Institute
44 Lincoln's Inn Fields
London WC2A 3PX

Telephone: 020 7269 3033
Fax:       020 7269 3258
E-mail: marcin.krol_at_cancer.org.uk

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