AMBER Archive (2008)

Subject: RE: AMBER: Heme cysteine

From: Shaikh Abdul R S Ramaju (
Date: Tue Oct 21 2008 - 21:46:09 CDT

Hello Dr. Ross,


Thanks a lot for the help. Its working now.



Abdul Rajjak


From: [] On Behalf
Of Ross Walker
Sent: Tuesday, October 21, 2008 11:17 PM
Subject: RE: AMBER: Heme cysteine


Hi Abdul,


Leap works by following the protein chain, adding bonds to the heads and
tails as it goes. Hence for the Fe the most it will ever do is add 2
bonds, it cannot work out the coordination itself so you have to add
these missing bonds manually. The reason you are getting the bond to the
backbone C of cysteine is that the Fe in your pdb file probably does not
have TER cards around it hence it tries to bond it into the backbone
chain. I suggest doing the following:


1) Change cysteines that bind to the Fe to be residue name CYM (This
prevents leap from adding the additional hydrogen on the sulphur.)

2) Modify any other residues that need to be modified / deprotonated
etc to bond to the iron - change their names in the pdb file to match.

3) Add TER cards either side of the Fe atom in the pdb file.

4) Load leap and the various leaprc and prepin / frcmod files you need.

5) load the pdb and then use the bond command to add the bonds you


Good luck,



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