[gmx-users] SwissParam itp files

[Albert]

It's not accurate enough. you'd better use Cgen FF from Gromacs.




On 06/08/2015 12:33 PM, soumadwip ghosh wrote:
> 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