RE: AMBER: heme forcefield atom types

From: Yang, Lee-Wei <>
Date: Wed, 24 Oct 2007 14:41:29 -0400

Dear Dr Cojocaru,

Thanks very much for your quick reply.

I followed your advice, put the HIS and HEM together, checked if the heme atom names in the PDB file agree with those defined in and I also added two hydrogen atoms to match exactly 55 atoms (excluding the 3 dummies) with

I also replaced all the HETATM cards to ATOM cards in the .pdb and deleted the SO4 ion.

Then, I did the following :

>>source leaprc.ff99SB (I really wanted to use leaprc.ff03ua but if I have done so, the WAT couldn't be recognized later on and gave the error message : )
>>loadamberparams /home/software/amber/amber9_patch34/dat/contrib/heme/frcmod.hemuni
>>loadamberprep /home/software/amber/amber9_patch34/dat/contrib/heme/
>>mbdo=loadpdb ./1MBD-mod.pdb
>>saveamberparm mbdo mbdo.crd

Unfortunately, the 'HEM' still could not be recognized and gave the error message as
I also uploaded my modified .pdb at
It will be very nice of you to tell me where it is done wrongly. Thanks again.


From: Vlad Cojocaru []
Sent: Wednesday, October 24, 2007 12:29 PM
To: Yang, Lee-Wei
Subject: Re: AMBER: heme forcefield atom types

Dear Yang,

You should specify in your pdb file that the histidine belongs to the
heme ... E.g. If the name of heme residue is HEM in your pdb file and in
the Leap library, you should change the name of the histidine residue
attached to the heme in your pdb file also to "HEM" ... (I would
actually move the HEM records from the end of the pdb next to the HIS
residue attached to it and have HIS+HEM a single residue called HEM)

You should also make sure that your atom names in the Leap library fits
100% to the atom names in your pdb file ...

 From your Leap error it looks as if you are not loading the water model
as well ....


L. W. Yang wrote:

> Dear John, Vlad, Professor Case and Amber experts,
> To study the dynamics of deoxy-Myoglobin, I wanted to take
> advantage of Amber 9_patch34's forcefield, dat/contrib/heme that is
> dedicated specifically for heme contained molecules. I'm new to Amber
> and also to heme-contained molecules. However, thanks for John and
> Vlad's conversation earlier and the suggestions from 0README.txt in
> the heme folder, I chose the united-atom version, frcmod.hemuni and
> for my molecule.
> not only defines the force and connectivity for heme but
> also the histidine that coordinates the FE(II) as a whole, so I wonder
> how I should tell the tleap that my histidine 93 actually belongs to
> part of the HEM (heme) group.
> If I simply run tleap on my PDB file as it is (except I delete the
> 'CONECT' cards in the PDB file), such as the following three-line
> commands, tleap was easy on me.
> >>source leaprc.ff03ua
> >>loadamberparams frcmod.hemuni.modified (where I added the demanded
> 'MASS' for it to run properly:
> NP 14.01
> NO 14.01
> CY 13.0
> CX 14.0
> CD 13.0
> FE 55.85
> LC 12.01
> LO 16.00
> HW 01.00
> CL 35.45)
> >>loadamberprep
> /home/software/amber/amber9_patch34/dat/contrib/heme/
> However, when I did the following 2 lines, the errors and warning
> messages appeared.
> >>mbdo=loadpdb ./1MBD.pdb (I have deleted data following the
> 'CONECT' cards)
> >>saveamberparm mbdo mbdo.crd
> -------- The Error message was too long. I put it at
> <> -------
> Can people suggest me how I should modify my PDB file for tleap?
> Also, for those successfully ran Amber (with provided heme forcefield)
> on deoxy-myoglobin structures, may I ask which PDB files do you use?
> Best regards,
> Lee

Dr. Vlad Cojocaru
EML Research gGmbH
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69118 Heidelberg
Tel: ++49-6221-533266
Fax: ++49-6221-533298
EML Research gGmbH
Amtgericht Mannheim / HRB 337446
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Received on Sun Oct 28 2007 - 06:07:12 PDT
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