[gmx-users] How to break a disulfide bond ???

[Venkat Reddy]

Thanks Sharada madam n justin sir for ur kind attention.I followed ur
command "pdb2gmx -ss".its asking like

Link CYS-37 SG-306 and CYS-59 SG-453 (y/n) ?n
Link CYS-44 SG-358 and CYS-50 SG-390 (y/n) ?y
Link CYS-72 SG-560 and CYS-101 SG-764 (y/n) ?y
Link CYS-82 SG-628 and CYS-93 SG-707 (y/n) ?y
Link CYS-150 SG-1137 and CYS-156 SG-1173 (y/n) ?y
Link CYS-203 SG-1546 and CYS-258 SG-1984 (y/n) ?y
Link CYS-210 SG-1603 and CYS-231 SG-1767 (y/n) ?y

actually i want to break the s-s bond between CYS37 n CYS59 . so i've given
the options like as shown above. When i again visualized the pdb in
pymol,its showing the disulfides as it is (no break between CYS37 n CYS59).
Can u suggest me wat to do ????
Thanks for giving reply.
On Fri, Mar 6, 2009 at 7:24 PM, sharada <sharada at ccmb.res.in> wrote:

> Do you intend to protonate a pair of cysteins and not make a SS bond?
> Then pdb2gmx -ss should do the job.
>
> Sharada
>
>
> *-- Original Message --*
> From: sharada <sharada at ccmb.res.in>
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Date: Fri, 6 Mar 2009 12:28:54 +0530 (IST)
> Subject: Re: Re: [gmx-users] How to break a disulfide bond ???
>
> If you donot make it, it is as good as breaking it...
>
> Sharada
>
> *-- Original Message --*
> From: Venkat Reddy <venkat4bt at gmail.com>
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Date: Fri, 6 Mar 2009 11:31:57 +0530
> Subject: Re: [gmx-users] How to break a disulfide bond ???
>
> Hai !
>
> with "pdb2gmx -ss", i can select the ss bonds. But after that, how to break
> a particular ss bond (not all).
> Thank you
>
>
> On Fri, Mar 6, 2009 at 11:01 AM, sharada <sharada at ccmb.res.in> wrote:
>
>>
>> pdb2gmx -h
>>
>> sharada
>>
>>
>>
>> *-- Original Message --*
>> From: Venkat Reddy <venkat4bt at gmail.com>
>> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>> Date: Fri, 6 Mar 2009 10:50:24 +0530
>> Subject: [gmx-users] How to break a disulfide bond ???
>>
>> Hai Every one ! Is it possible to break a disulfide bridge using gromacs
>> ?????If so,Can anybody suggest me, how to do it???
>>
>> Thanks for ur valuable time
>>
>> With best wishes
>> Venkat Reddy Chirasani
>> M.Tech Bioinformatics
>> UNIVERSITY OF HYDERABAD
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>
>
>
> --
> Venkat Reddy Chirasani
> M.Tech Bioinformatics
> UNIVERSITY OF HYDERABAD
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-- 
Venkat Reddy Chirasani
M.Tech Bioinformatics
UNIVERSITY OF HYDERABAD
Laboratory of Computational Biology
Centre for DNA Fingerprinting and Diagnostics
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