Le Tuesday 20 December 2011 à 12:18:51AM, Jan-Philip Gehrcke a écrit :
> Jeff, please see below.
>
> On 19.12.2011 23:22, Jeffrey Thalhammer wrote:
> >
> >On Dec 19, 2011, at 1:39 PM, Lachele Foley (Lists) wrote:
> >
> >>The code is getting a little old, so do let me know if you find
> >>something that doesn't work. But, there is a tool here:
> >>
> >>http://glycam.ccrc.uga.edu/ccrc/GlycamLITE/Protein/uploadIndex.jsp?option=ff99
> >
> >>
> >Yes, that's exactly what I had in mind. I see that it does a nice
> >job of removing the hydrogens and zeroing/stripping the columns that
> >Amber doesn't want. But the cysteine residues are still CYS rather
> >than CYX.
>
> You only want to have those CYS residues "cyxified" that take part
> in disulfide bonds, so you have to check manually. After
> cyxification in the PDB and loading the PDB file into leap, you have
> to covalently bind the CYX pairs that build up disulfide bonds. My
> workflow is like that (in the shell):
>
> 1) Print residue numbers of cysteins
> ====================================
> $ cyslist 2ILK.pdb
> 12 62 108 114
>
> 2) Verify disulfide bonds with literature
> =========================================
>
> 12 bridges to 108
> 62 bridges to 114
You can also read which CYS are engaged in a disulfide bond from the PDB
headers (SSBOND entries) and rename them to CYX automatically.
$ grep SSBOND 3EAC.pdb
SSBOND 1 CYS A 122 CYS A 164 1555 1555 2.03
...
--
Thomas Gaillard
Maître de conférences
Laboratoire de Biochimie
Ecole Polytechnique
91128 Palaiseau cedex
tel: +33 1 69 33 48 62
fax: +33 1 69 33 49 09
thomas.gaillard.polytechnique.edu
http://bioc.polytechnique.fr/~gaillard
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Received on Mon Dec 19 2011 - 17:00:03 PST
