AMBER Archive (2009)

Subject: Re: [AMBER] S-S problem-in protein

From: Jason Swails (jason.swails_at_gmail.com)
Date: Sun Oct 11 2009 - 21:15:10 CDT

Rilei,
Leap adds hydrogens by default according to a template in all_amino94.lib,
which is designed to make the process of creating topology files from PDBs
easy. However, this makes the different protonation states of various
residues slightly more complex (i.e. different protonation states of
Histidine, Aspartate, Glutamate, etc.). Thus, each protonation state is
given its own residue name. Cysteine, too, can either be a free residue
capped by a hydrogen, or it can be involved in a disulfide bond with another
cysteine (yielding a cystine). Thus, a free cysteine has the 3-letter code
CYS, but each cysteine member of a cystine (cysteine dimer) has the 3-letter
code CYX according to all_amino94.lib. Therefore, if you wish to change
your cysteines into cystines, change each CYS in the pdb into CYX.

In this detail, I may be mistaken, so somebody please correct me if I am, I
am drawing from recollection of my own experiences adding S-S bonds. If you
are using tleap or xleap, you will have to manually add the S-S bonds
(either through the 'bond' command detailed in the ambertools manual, or by
hand in xleap if that's possible, I've never tried that approach). However,
if you use sleap, I believe that it adds the disulfide bonds for you.

Hope this helps,
Jason

2009/10/11 Rilei Yu <yulaomao1983_at_yahoo.com.cn>

> Dear amber users,
>
> When i load my protein that contains 7 S-S,I found the these disufides
> bonds were all open, and one hydrogen is linked to the "S"-atom terminal, so
> I edit them in the xleap one by one, it is really time consuming, because I
> will edit many such complex! Do anyone know is there any better approach to
> solve this problem?
>
> Thanks for your help!
>
> Rilei Yu
>
>
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-- 
---------------------------------------
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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