[gmx-users] lipid.itp LJ-1,4 values involving water

[chris.neale at utoronto.ca]

Does anyone know why lipid.itp contains [pairtypes] LJ-1,4 values including
lipid atoms and OW or HW? I can understand their inclusion in [nonbond_params],
but it seems as if this would never be required in [pairtypes].

***

In case anyone else is trying to merge lipid.itp and OPLSAA, here is what I have
done. There is no type of guarantee here, just a listing of what appears to be
working so far for me.

Download lipid.itp and pope.itp (or your lipid) from
http://moose.bio.ucalgary.ca/ kindly made available for all by Dr. Peter Tieleman.

1. Added [atomtypes] from lipid.itp to ffoplsaanb.itp -- after changing c6/c12
to sigma/epsilon. Also added atomtype H from olsa_369 to match H expected by
pope.itp
  - sigma   = (c12/c6)^1/6
  - epsilon = c6/(4*sigma^6)

2. Added [pairtypes] from lipid.itp to ffoplsaanb.itp -- after changing c6/c12
to sigma/epsilon. (gives effective fudgeLJ of 0.125). Also changed all reference
to OW to opls_116 (opls spc water oxygen) and simply removed any with reference
to HW as it will be zero regardless.

3. Added [dihedraltypes] from lipid.itp to ffoplsaabon.itp. 
  - Prior to running ensure that the non-RB dihedral does not exist for these
groups.

4. make a topology file like this:

#include "ffoplsaa.itp"
#include "myprotein.itp"
#include "spc.itp"
#include "pope.itp"

[ system ]
system_name

[ molecules ]
; Compound        #mols
Protein             1
POPE              299
SOL              8991