AMBER Archive (2008)

Subject: Re: AMBER: disulfide bridge with ff03ua FF

From: Ray Luo (rluo_at_uci.edu)
Date: Tue Feb 12 2008 - 16:52:37 CST

Marcin,

This is because ff03ua was not developed with CYX, i.e. the cys for
disulfide bond. Since all ff03aa/ff03ua parameters are from ff99, you
can make up your own frcmod file for the missing parameters by
borrowing the corresponding ff99 parameters for CYX. Keep in mind
that CT in ff99 is either C3 (CH3), C2(CH2) or C1(CH) in ff03ua.

All the best,
Ray

On Feb 8, 2008, at 9:00 AM, Marcin Krol wrote:

> 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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> The AMBER Mail Reflector
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