[gmx-users] Wild ffgmx forcefield
bmbbl at bmb.leeds.ac.uk
Wed Apr 13 19:27:03 CEST 2005
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.
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