[gmx-users] help on converting charmm/cgenff parameters to gromacs

[Peter C. Lai]

Hello

I am constructing a ligand for which I wish to use the new Charmm CGenFF 
parameters (a long aliphatic ketone).

I am using Tom/Par's charmm36 lipid conversion as a baseline template for
comparison:

For reference, c36 lipid CTL3 atoms (in the case of POPC) map to CG331 
in CGenFF; they are both to represent alkane CH3 carbons. Same with
CTL2 -> CG321. In my case I am particularly interested in CGenFF's 
parameterization of a ketone carbonyl and oxygen: CG2O5 and OG2D3 
(without any associated carboxylic bias or bias from non-carbons found
in other parameters. For example C=O in amino acid backbone appears in
ffbonded.itp as 5.188e+05 for kB whereas Mark's script yielded a kB of 
5.858e+05 for CG2O5=OG2D3, not to mention the bond angles should be 
different and especially the nonbonded interactions since we've replaced
N with C and we have an extra H etc. etc.).

My ligand for now is pretty simple:

                      OG2D3
                       ||
CG331-CG321-...-CG321-CG2O5-CG331

or, in c36 lipid/prot terms:
                   O  
                   ||
CTL3-CTL2-...-CTL2-C-C-CTL3

How would I convert the relevant atoms in CGenFF's prm file to both 
dihedral and nonbonded interaction .itp for gromacs? I tried using Mark's 
perl scripts and it is giving me wrong LJ terms as well as not picking up 
any 1,4 interactions (not to mention it has no knowledge of Par's 
functype 9 for converting Charmm dihderals - we should no longer be using
R-B functions).

Finally, a slightly (un)related question:
in ffnonbonded.itp, why does CTL2 get a charge of 0.05 when in reality we
usually give it -0.18 for associated molecules in the rtp? Is there 
something I'm missing there? (CTL3 has -0.27 in both the itp and rtp files
which makes sense to me).

-- 
===============================================================
Peter C. Lai                 | University of Alabama-Birmingham
Programmer/Analyst           | BEC 257
Genetics, Div. of Research   | 1150 10th Avenue South
pcl at uab.edu                  | Birmingham AL 35294-4461
(205) 690-0808               |
===============================================================