Re: AMBER: heme forcefield atom types

From: L. W. Yang <>
Date: Thu, 25 Oct 2007 01:18:31 +0900

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,


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Received on Sun Oct 28 2007 - 06:07:10 PDT
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