[gmx-users] RE: heme / specbond.dat

Tsjerk Wassenaar t.a.wassenaar at chem.rug.nl
Thu Jan 16 15:13:40 CET 2003

Dear Mr. Prabhakaran,

The problem is in the file specbonds.dat in the top directory (usually 
This file contains entries for less straightforward connections between 
residues and molecules. The file will probably look as follows:



CYS	SG	1    CYS	SG	1    0.2	CYS2    CYS2

CYS	SG	1    HEME	FE	2    0.25	CYS2    HEME

CYS	SG	1    HEME	CAB	1    0.18	CYS2    HEME

CYS	SG	1    HEME	CAC	1    0.18	CYS2    HEME

HIS	NE2	1    HEME	FE	1    0.2	HIS1    HEME


The connections are based on a distance matrix and will only be formed when the distance between the atoms is shorter than a maximum distance given in this file, which is the number in the 7th column. In the case of 1HRC the distances of two of the bonds are larger than the given number and are the atoms thus not connected. This concerns the bonds between the methionine and the sulfur and between HEME CAB and cysteine.
Increasing the maximum allowable distance between the atoms slightly should be enough to get things connected in the right way, for example 0.19 nm for the SG-C bonds.

For methionine a line should be added defining the bond between the sulfur and the iron.

The attached specbonds.dat should enable you to correctly convert 1HRC.pdb. Though I should add that I have not added the extra angle and dihedral terms. When needed, these can be added manually in the topology file. Also, the charges on the methionine may deviate from the normally used value in the force-field due to binding to iron.
Place the file in the 'current working directory'.

I hope this is of any help. For future questions I might suggest you to revert to the Gromacs user list to which you can subscribe at www.gromacs.org. There a lot of users can comment on problems which are encountered and there's an archive in which answers can be sought to those common problems.

Sincerely yours,

Tsjerk Wassenaar

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