[gmx-users] specbonds are not taken by gromos force field?

라지브간디 rajiv at kaist.ac.kr
Tue Apr 23 15:36:36 CEST 2013

Dear Justin,

Sorry for the confusion.

What I was trying to explain is " pdb2gmx output of topol.top file shows the detection of heme (FE) bound with histidine (NE2) atom but missing to mention the gromacs bond, angle, dihedral type code.

Which clearly means that pdb2gmx to not able detect the gromacs bond type code to assign their parameters...

I have checked the parameter of this heme-his and its found like this :


#define gb_34        0.198   0.6400e+06
; NR  -   FE    120


#define ga_17       115.00       50.00; NR(heme)  -  FE  - NR 10
#define ga_34       125.00      375.00; FE  - NR  - CR1 (5-ring)
dihedral#define gd_38     0.000        0.0          4; -NR-FE-       0.0

Could you tell how do make pdb2gmx to assign this parameter ? Thanks in advance.

Can you please provide an exact example of what the issue is? Your question 
conflicts itself - first you say the parameters are not looked up in 
ffbonded.itp, but then you say the parameters are there. There are frequent 
reports of issues with heme in Gromos96 force fields, but none ever seem to get 
resolved, usually due to lack of information. 


On 4/19/13 10:45 AM, ��������������� wrote: 
> Hello gromacs. 
> I wanna simulate the heme contain proteins which has bond FE-NE2 from HIS as it already found in specbond section. 
> When i use pdb2gmx, I could see the links of these but in topology file but not parameter information which detects from ffbonded.itp. 
> I also checked the ffbonded.itp file and found that it has default parameter information for heme links with his, which also described in specbond column. 
> What can be done to pdb2gmx to detect these bond parameter from ffbonded.itp file? 

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