RE: AMBER: Heme cysteine

From: Ross Walker <>
Date: Tue, 21 Oct 2008 08:17:08 -0700

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 require.


Good luck,



From: [] On Behalf Of
Shaikh Abdul R S Ramaju
Sent: Tuesday, October 21, 2008 12:17 AM
Subject: AMBER: Heme cysteine


Dear Amber users,


As I have previously posted the error message while preparing the input file
for heme-cysteine group.

Unfortunately I didn’t received any answer. Now my question is does tleap
program can identify the coordination number of Fe in heme?

I tried to prepare topology file for five coordinated heme group (heme
attached to cysteine). In this sytem it is giving error that “WARNING: There
is a bond of 4.890173 angstroms between:

------- .R<HEM 357>.A<FE 9> and .R<HEM 357>.A<C 82>”. Although this bond
does not exist (Fe and backbone C of cysteine), why program is showing error
message about this bond. After manual deleting this bond, it does not show
error. Then when I tried to save the .top and .crd file, after the “Marking
per-residue atom chain types.” System get hang and it does not save the
topology and coordinate files.


On the other hand, when I use a six coordinated Fe in which water is the
sixth ligand, and add the parameters for water in prep and frcmod file, it
works fine. I could able to save the topology file.

I am unable to understand what will be the reason behind this two system.



I shall be thankful for any suggestion or comments in this regard.


Best regards


Abdul Rajjak




Dear Dr. Ross,


While preparing the Cytochrome P450, first I added the missing residues
using swiss pdb viewer. The I added hydrogen to HEM and cysteine group,
which is also attached to heme (I didn’t added the hydrogen to protein, as
leap does not recognize it). Then I took the parameters from amber
contributed parameters (amber9/dat/contrib). As parameters are for
heme-histidine, I modified it for heme-cysteine. After that I used usual
procedure using tleap.

Set of commands are as follows-

source leaprc.ff99

loadamberparams parm99_mod.dat

loadamberparams frcmod.heme_all


mol=loadpdb 2H7S_mod.pdb

check mol


After check mol I got error message that FE is bonded to backbone C of
cysteine. According to one of the Amber users suggestion, I deleted that
bond using deletebond command. Then I didn’t find the error about bond
between FE and C. Finally I tried to save topology file using saveamberparm.
After “Marking per-residue atom chain types.” System get hang at this point.
No error message is found after this sentence. In my previous message I have
attached the pdb files and parameter files
( Please find the attached file
for commands and error message.


Thanking you


Abdul Rajjak



From: [] On Behalf Of
Ross Walker
Sent: Wednesday, October 08, 2008 11:23 PM
Subject: RE: AMBER: saveamberparm error


Dear Shaikh,


I don't see any error message in your output below. What exactly do you mean
by the "System gets stuck"? Does it just hang at this point?


Can you send us your full set of leap commands, I.e. what you did before the
saveamberparm, as well as a more in-depth discussion of the pdb you used,
how you modified it, what parameters you are using etc. and then we might be
able to work out what is going on.


All the best



From: [] On Behalf Of
Shaikh Abdul R S Ramaju
Sent: Wednesday, October 08, 2008 4:34 AM
Subject: AMBER: saveamberparm error


Dear Amber Users,


I am trying to prepare amber input files for Cytochrome P450.

When I tried to save to topology file and coordinate file, following message
appears. After “Marking per-residue atom chain types.” System gets stuck. It
didn’t create any topology file. What will be the possible reason for this
error. I will be grateful for your suggestion.



Abdul Rajjak


> saveamberparm mol parmtop parmcrd

Checking Unit.

WARNING: The unperturbed charge of the unit: -20.000000 is not zero.


 -- ignoring the warning.


Building topology.

Building atom parameters.

Building bond parameters.

Building angle parameters.

Building proper torsion parameters.

Building improper torsion parameters.

old PREP-specified impropers:

 <HEM 357>: -M CA N H

 <HEM 357>: CA +M C O

 <HEM 357>: NA C1A C4A FE

 <HEM 357>: NB C1B C4B FE

 <HEM 357>: NC C1C C4C FE

 <HEM 357>: ND C1D C4D FE

 <HEM 357>: C1A C2A NA CHA

 <HEM 357>: C1B C2B NB CHB

 <HEM 357>: C1C C2C NC CHC

 <HEM 357>: C1D C2D ND CHD

 <HEM 357>: C2A C3A C1A CAA

 <HEM 357>: C2B C3B C1B CMB

 <HEM 357>: C2C C3C C1C CMC

 <HEM 357>: C2D C3D C1D CMD

 <HEM 357>: C3A C4A C2A CMA

 <HEM 357>: C3B C4B C2B CAB

 <HEM 357>: C3C C4C C2C CAC

 <HEM 357>: C3D C4D C2D CAD

 <HEM 357>: C4A NA C3A CHB

 <HEM 357>: C4B NB C3B CHC

 <HEM 357>: C4C NC C3C CHD

 <HEM 357>: C4D ND C3D CHA

 <HEM 357>: C4D C1A CHA HGM

 <HEM 357>: CAC HT3 CBC HC4

 <HEM 357>: C3C CBC CAC HV4

 <HEM 357>: CAB HT7 CBB HC8

 total 1310 improper torsions applied

 26 improper torsions in old prep form

Building H-Bond parameters.

Not Marking per-residue atom chain types.

Marking per-residue atom chain types.

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Received on Wed Oct 22 2008 - 05:10:26 PDT
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