[gmx-users] cgenff generated force field problem

[Prabir Khatua]

Hi Gromacs Users,

I am trying to do a protein-ligand simulation where the force field of the
ligand has been generated by cgenff. I have manually edited the protein
.top file, which has been generated  by pdb2gmx, by adding the lines
#include .prm and #include .itp at appropriate positions. However, I am
getting a list of warning while I am trying to prepare .tpr file like

WARNING 10 [file lau.prm, line 43]:
  Overriding Proper Dih. parameters.
  Use dihedraltype 9 to allow several multiplicity terms. Only consecutive
  lines are combined. Non-consective lines overwrite each other.

  old:                                          0 0.452709 4 0 0.452709 4
  new: CG321    CG321    CG321    CG331     9     0.000000     0.853118
5

After careful examination, I have come to know that this is happening due
to the fact that these are already there in the parent force field file.
However, I have some dihedral angle force field parameters for the ligand
with same atom type, multiplicty as that of the protein but a slight
variation in the value of kphi. Therefore, I think I probably have to
delete the lines that are exactly matching with that of parent protein
force field from the ligand prm file and to keep the lines those are not
matching. I am wondering whether doing this will solve my problem and will
not have any impact on the results. Please suggest me whether I am going to
do the right thing or I should do something else. Any help would be
appreciated.

Thanks in advance,

Prabir
-- 

*Prabir Khatua*
*Postdoctoral Research Associate*
*Department of Chemistry & Biochemistry*
*University of Oklahoma*
*Norman, Oklahoma 73019*
*U. S. A.*