AMBER Archive (2008)

Subject: Re: AMBER: disulfide bridge with ff03ua FF

From: raja pandian (chemistryraj_at_gmail.com)
Date: Fri Feb 08 2008 - 10:17:50 CST

Hello Amber user,

                           Sir,
                                I got your problem, it is very simple thing
only. please create leap.in file.
Like.......,leap.in(file name)

              bond pdb.3.SG pdb.26.SG(after loading .frcmod file and
.prepinfile with in the file)

Then you will load leap.in file as a source file at xleap....
After wise you can edit the file name at xleap ...definitely the the
disulfide bridge is formed

Thanking You

On Feb 7, 2008 8:20 PM, Marcin Krol <krol01_at_cancer.org.uk> wrote:

> Hello
>
> > I want to create a disulfide bridge using ua ff, but there is no CYX
> > residue type. When I tried with CYS leap complained about missing
> > parameters for SH-SH bond and angles. In fact, there are no such
> > parameters in frcmod.ff03ua. Does it mean that I can't have disulfide
> > bridges in ff03ua?
> >
> > Thanks in advance for your answers
> > Marcin
> >
>
>
> --
> 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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