[gmx-users] GROMOS96 and protein-ligand complex

[Outi Maija Salo]

Hi!


We have some problems in preparing a normal MD run for a protein-ligand
complex.
We prepared the ligand .itp and .gro files in PRODRG server.
THen we added these files to corresponding .gro file and .top file of the
protein just as we have previously done and it worked then.

We chose to use the GROMOS96(ffG43a1) force field (this was new to
previous work).

The first problem occurred when we tried to use grompp:

Fatal error: Atomtype 'CR61' not found!

Well, this atom type was not in ffG43a1.atp. So, we changed this and some
other atom types to the corresponding types of this force field.

Our ligand has the name LIG.
The next error message from grompp was the following:


 WARNING 2 [file "top_ligand.top", line 18689]:
  atom C35 (Res LIG-301) has mass 0

WARNING 3 [file "top_ligand.top", line 18689]:
  atom C34 (Res LIG-301) has mass 0

WARNING 4 [file "top_ligand.top", line 18689]:
  atom C33 (Res LIG-301) has mass 0

WARNING 5 [file "top_ligand.top", line 18689]:
  atom O36 (Res LIG-301) has mass 0

WARNING 6 [file "top_ligand.top", line 18689]:
  atom HAA (Res LIG-301) has mass 0

WARNING 7 [file "top_ligand.top", line 18689]:
  atom C32 (Res LIG-301) has mass 0

WARNING 8 [file "top_ligand.top", line 18689]:
  atom C31 (Res LIG-301) has mass 0

WARNING 9 [file "top_ligand.top", line 18689]:
  atom C30 (Res LIG-301) has mass 0

WARNING 10 [file "top_ligand.top", line 18689]:
  atom C29 (Res LIG-301) has mass 0

...

What is the problem? Is the GROMOS96 ff not suitable for protein-ligand
complexes or should we change some ff parameters e.g. in ffG43a1nb.itp
file? We really could not find the reason for this...

Thanks for your help!

Outi Salo
University of Kuopio
Finland