[gmx-users] SwissParam itp files

[Justin Lemkul]

On 6/8/15 6:33 AM, 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:
>

Do you have some reason to think that the affinity should be larger?  The 
representation (assuming, from the snippets of the topology) of the fullerene is 
such that it only interacts with LJ interactions.  Charges dominate in water, so 
if the binder has polar moieties it is likely to have weak affinity for the 
fullerene and stronger affinity for water.  Unless there are experimental data 
suggesting this interaction should be stronger, what you are seeing is simply 
consistent with a weak binding affinity.

> 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
>

Note that [pairtypes] are intramolecular interactions.  They have no implication 
for intermolecular nonbonded interactions.

> 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

You're overriding an atomtype with itself.  This is not a problem here at all. 
This is not causing any error.  grompp warns you of the possibility of a 
mistake, in case you have different parameters in different topologies.  This is 
not the case here.

-Justin

> 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
>

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==================================================