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

라지브간디 rajiv at kaist.ac.kr
Fri Apr 19 16:45:52 CEST 2013

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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