[gmx-users] breaking S-S bond using pdb2gmx

[Sahithya S Iyer]

Thanks for the reply Justin.

yes, i do notice the topology files have the S-H bonds.

On Mon, Feb 16, 2015 at 6:10 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 2/16/15 4:27 AM, Sahithya S Iyer wrote:
>
>> Deal all,
>> I need to break 1 out of 4 S-S bonds in a protein. While using the pdb2gmx
>> command, i used -ss whereby i was asked which S-S bonds i would what to
>> keep intact and which i'd break. Since i wanted the S-S bond between CYS
>> 6-CYS 127 to be broken, i gave he following command -
>> Link CYS-6 SG-48 and CYS-127 SG-981 (y/n) ?n
>> Link CYS-30 SG-238 and CYS-115 SG-889 (y/n) ?y
>> Link CYS-64 SG-513 and CYS-80 SG-630 (y/n) ?y
>> Link CYS-76 SG-601 and CYS-94 SG-724 (y/n) ?y
>> The .gro file generated , visualised using vmd, shows 4 S-S bonds instead
>> of 3. Where have i gone wrong. Is there any other method the break the S-S
>> bonds present in the pdb file ?
>>
>
> The topology is definitive, not what you see in VMD.  Though the -SH
> groups should be obviously present.  Make sure you're visualizing the right
> file.
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
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>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
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-- 
Sahithya S Iyer