[gmx-users] SwissParam itp files

[soumadwip ghosh]

Dear users,

                 I am trying to see the interaction between fullerene and
water soluble binders using GROMACS 4.5.6 and CHARMM 27 all atom force
field. I made the topology by SwissParam web server for both fullerene and
the organic binder and my topology file looks like this-

GROMACS topology
;
; Include the force field
#include "charmm27.ff/forcefield.itp"

;Include CHARMM atomtypes
#include "atomtypes_fullerene.itp"
#include "atomtypes_binder.itp"

; Include chain topologies
#include "fullerene.itp"
#include "binder.itp"

; Include water topology
#include "charmm27.ff/tip3p.itp"

#ifdef POSRES_WATER
; Position restraint for each water oxygen
[ position_restraints ]
;  i funct       fcx        fcy        fcz
   1    1       1000       1000       1000
#endif

; Include generic ion topology
#include "charmm27.ff/ions.itp"

[ system ]
Fullerene in water

[ molecules ]
LIG             1
GAC             5
SOL             607

I have kept the entire system in a cubic box along with explicit tip3p
water molecules. Now in principle the two residues should get stacked and
the corresponding interaction should be reflected in the md.edr file,
right? But in my case neither the last md.gro file exhibit any kind of
stacking nor the Eint is large (-8-9 kJ/mol). I want to know why is it
happening? As far as I know, SwissParam topologies are fairly reliable in
connection with CHARMM 27 force fields? The atomtypes files are as follows:

For fullerene

[ atomtypes ]
; name at.num  mass   charge  ptype    sigma            epsilon
CB      6   12.0110  0.0  A         0.355005    0.292880


[ pairtypes ]
;  i     j    func     sigma1-4       epsilon1-4 ; THESE ARE 1-4
INTERACTIONS

And for the binder,

[ atomtypes ]
; name at.num  mass   charge  ptype    sigma            epsilon
CB      6   12.0110  0.0  A         0.355005    0.292880
HCMM    1    1.0079  0.0  A         0.235197    0.092048
OR      8   15.9994  0.0  A         0.315378    0.636386
C=O     6   12.0110  0.0  A         0.356359    0.460240
O=C     8   15.9994  0.0  A         0.302905    0.502080
HOCC    1    1.0079  0.0  A         0.040001    0.192464
HOCO    1    1.0079  0.0  A         0.040001    0.192464


[ pairtypes ]
;  i     j    func     sigma1-4       epsilon1-4 ; THESE ARE 1-4
INTERACTIONS
O=C      CB     1      0.302228    0.383470
O=C      HCMM   1      0.242324    0.214978
O=C      OR     1      0.282415    0.565258
O=C      C=O    1      0.302905    0.480705
O=C      O=C    1      0.249452    0.502080
O=C      HOCC   1      0.144726    0.310857
O=C      HOCO   1      0.144726    0.310857

There was one warning though whenever I issued grompp that ' atomtypes CB
has been overridden' which was ignored as I thought it was not harmful and
the same was also suggested by Justin. Is this the reason why the correct
interactions are not arising or something else is missing here? If
overriding of atomtypes are the drawback every time I call grompp, what is
the possible way out to ensure correct molecular interactions. For
information I equilibrated the system for 300 ps and 5 ns in NVT and NPT
respectively and the production run was for 50 ns.

Thanks for your help in advance.

Soumadwip Ghosh,
Research Fellow,
IITB
India