[gmx-users] problems with Cysteines

Steve stevesei at ymail.com
Fri Jan 17 20:48:57 CET 2014

I have attempt to make present in my confout.gro structure both CYSH and CYS.
I was able to do so, but only by modifying the FF (renaming CYS to CYX in
both my pdb file and the forcefield used). If I took out the HG hydrogen in
pdb and left the name as CYS in forcefield, pdb2gmx would add a HG atom to
confout.gro automatically.

According to what I have read in manual and on-line is that if I do the

$pdb2gmx -f name.pdb -ss -his

I should be able to select what cysteines and histidines I what protoned

HOWEVER, when I do this the code pdb2gmx lets me select His, but does not
allow any changes to Cys (to make s-s bonds or anything). Am I doing
something wrong here?

Could someone please tell me what I can do to make a S-S bond...do I have to
use "specbond.dat"???

Thanks, Steve

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