AMBER Archive (2008)

Subject: Re: AMBER: disulfide bridge with ff03ua FF

From: Marcin Krol (krol01_at_cancer.org.uk)
Date: Fri Feb 08 2008 - 11:00:25 CST

Thanks
I actually tried to do the bond command in leap, but with ff03ua it
complains about missing parameters.
Marcin
> Hello Amber user,
>
> Sir,
> I got your problem, it is very simple
> thing only. please create leap.in <http://leap.in> file.
> Like.......,leap.in <http://leap.in>(file name)
>
> bond pdb.3.SG <http://pdb.3.SG> pdb.26.SG(after loading
> .frcmod file and .prepin file with in the file)
>
> Then you will load leap.in <http://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
> <mailto: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 <mailto:marcin.krol_at_cancer.org.uk>
>
>
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> 

-- 
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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