AMBER Archive (2008)

Subject: Re: AMBER: disulfide bridge with ff03ua FF

From: Marcin Krol (krol01_at_cancer.org.uk)
Date: Wed Feb 13 2008 - 09:32:18 CST

Thanks Ray,
That's what I did - I modified frcmod.ff03ua by adding parameters for
angles and dihedrals involving S and C2 based on param99. I also added
CYX residue to uni_amino03.lib, a bit tricky because I don't know the
format of lib files, but know it seems to work and produces reasonable
geometries.
Best
marcin
> 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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>
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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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