[gmx-users] ligand topology

[Mohammad Zahidul Hossain Khan]

Dear Sir

I am new for protein-ligand complex. I want amber force field (ff03) for my
protein, tip3p for water model and gaff (General Amber force field) for
ligand. I do not know how to produce gaff force field from pdb and then
convert for gromacs topology.

I have tried ff03 with gromos ligand topology and tip3p water model

it gives me the error:
atomtype OM not found

and when I have tried ff03 with gromos topology and spc water model it
gives me the error like:
atomtype HW not found.

Can anyone help me about it?

-- 


*Mohammad Zahidul Hossain Khan Graduate student**Department of Physics*
*Email: khan5121 at vandals.uidaho.edu <khan5121 at vandals.uidaho.edu>*
* Skype: parash.khan2*
*Cell: +12085967165*