Re: CYS and HIS

From: <>
Date: Wed, 16 Apr 2003 07:55:55 -0700 (PDT)

Leap does not add disulfide bonds automatically, you must
do this with the "bond" command.


On Wed, 16 Apr 2003, Youyi Peng wrote:

> Hi,
> My protein contains a disulfide bond and a HIS is involved in the
> ligand binding. I renamed the corresponding CYS and HIS to CYX and HIE
> in the pdb file and then loadpdb into xleap and saved the prmtop and
> inpcrd files. S-S disulfide bond existed in inpcrd file. After energy
> minimization, S-S bond broke up and the distance is over 3 A in the
> min.restrt file. It seems to me that loadpdb treats CYS as a residue
> name but not the real CYS (including S-S bond). Am I Rright? what is the
> normal procedure to deal with CYX and HIE(D/P)?
> I have questions here:
> For CYS, even I changed the res. name, I still need to use BOND to make
> the bond in leap and loadpdbusingseq, Or loadpdb will treat CYX as the
> defined CYX by AMBER?
> For HIS, after I changed the name to HIE, when loaded into leap, it is
> treated as HIE or still the default HIS? Do I need to change the leaprc
> file?
> I am an AMBER beginner, If I ask some silly and simple questions,
> please don't feel mad at me.
> Thanks a lot.
> Youyi Peng

James W. Caldwell                         (voice) 415-476-8603
Department of Pharmaceutical Chemistry    (fax)   415-514-3866  
UCSF Box 2240                             (email)
600 16th Street
University of California
San Francisco, CA 94143-2240
Received on Wed Apr 16 2003 - 16:53:01 PDT
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