[gmx-users] Problems with pdb2gmx simulating a iron-sulfur cluster

[martinez]

Thank you for your reply Tsjerk

I have already edited my spec bond.dat file as follows

14
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	   0.2		CYS2	HEME
CYS	SG	      1      HEME	CAC	   1	   0.2		CYS2	HEME
HI2 	NE2	      1      HEME	FE	   1	   0.2		HIS1		HEME
CYS     SG      1       FS4     FE1     1       0.23     	CS- 		FS4
CYS     SG      1       FS3     FE1     1       0.23     	CS- 		FS3
CYS     SG      1       FS4     FE2     1       0.23     	CS-		 FS4
HIS	   ND1    1       FS4	FE2     1	   0.20	 HI2		 FS4
CYS     SG      1       FS3     FE2     1       0.23     	CS-     	FS3
CYS     SG      1       FS4     FE3     1       0.23    	 CS-     	FS4
CYS     SG      1       FS3     FE3     1       0.23     	CS-    	 FS3
CYS     SG      1       FS4     FE4     1       0.23     	CS-    	 FS4
CYS     SG      1       FS3     FE4     1       0.23     	CS- 		FS3

so that pdb2gmx can make bonds between the different residues.
I also edited my ff...bon.itp file to specify the bondtypes/angletypes 
but my problem is that  pdb2gmx does not specify the bondtype/angletype 
in the topology file, so I guess I did something wrong when I specified 
the bontypes,etc.. in the ff...bon.itp file. How does pdb2gmx "find" 
the bondtype/angletype for these special bonds in the ff...bon.itp 
file?
For the histidine ligand, what i had to do is edit the pdb and rename 
the his residue that bonds iron HI2, I couldn't get the histidines in 
the special atom matrix.

Thanks in advance