[gmx-users] Wild ffgmx forcefield

Binbin Liu bmbbl at bmb.leeds.ac.uk
Wed Apr 13 19:27:03 CEST 2005

Dear all,

I am trying to work out binding free energy difference of varying different 
Histidine protonation state.
 ffgmx force field is applied. I use DUM in the initial state in stead of HD1 
in the final state to do perturbation. Certainly I have to modify the 
topology of histine. I copy the topology of HISB and HISH from ffgmx.rtp to 
my own topol.top. 
First I simply copied both parameters and added HD1 in stateB. But grompp does 
not allow ffgmx format. So I tried to use the format what is used as examples 
in the manual. Surprisingly, there is no dihedral angle (function type 1) 
parameters in ffgmx.rtp. 
Second in  ffgmxbon.itp. The [dihedraltype] only gives information on 
i    l func        q0          cq, which I think it should be like i  j k l 
func phi cp mult. 
Does any one know what is the problem? Is my understanding wrong? Or where I 
can find out histidine topology information for ffgmx force field.

Thank you.


More information about the gromacs.org_gmx-users mailing list