[gmx-users] charmm to gromacs

[Justin Lemkul]

On 12/4/14 1:59 PM, Rebeca García Fandiño wrote:
> Dear Gromacs users,
> I am trying to obtain the .itp files for an organic molecule for a MD simulation in GROMACS using the CHARMM force field.
>
> I am trying to use cgenff_charmm2gmx.py:
>
> python cgenff_charmm2gmx.py MOL1 ligand.mol2 ligand.str charmm36-nov2014.ff
>
> After this step, I obtain several files, among them:
> mol1.top:
> ----------------------------------------
> #include "charmm36-nov2014.ff/forcefield.itp"
>
> ; additional params for the molecule
> #include "mol1.prm"
>
> #include "mol1.itp"
>
> #include "charmm36-nov2014.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 topology for ions
> #include "charmm36-nov2014.ff/ions.itp"
>
> [ system ]
> ; Name
> mol
>
> [ molecules ]
> ; Compound        #mols
> MOL1          1
> ----------------------------------------------------
>
> The file mol1.prm does not contain any value:
>
> -------------------------------------
>
> [ bondtypes ]
> ;      i        j  func           b0           kb
>
>
> [ angletypes ]
> ;      i        j        k  func       theta0       ktheta          ub0          kub
>
>
> [ dihedraltypes ]
> ;      i        j        k        l  func         phi0         kphi  mult
>
>
> [ dihedraltypes ]
> ; 'improper' dihedrals
> ;      i        j        k        l  func         phi0         kphi
>
> --------------------------------
>

This means your stream file did not introduce any new parameters.

>
> And in the mol1.itp file also obtained from cgenff_charmm2gmx.py, the values of c0, c1, c2, c3,...in bonds, angles, and dihedrals are missing:
>
> ----------------------------------
>
> [ bonds ]
> ;  ai    aj funct            c0            c1            c2            c3
>      1     2     1
>      1   108     1
>      1   109     1
>      1   110     1
> (...)
> [ angles ]
> ;  ai    aj    ak funct            c0            c1            c2            c3
>      2     1   108    5
>      2     1   109    5
>      2     1   110    5
>    108     1   109    5
> [ dihedrals ]
> ;  ai    aj    ak    al funct            c0            c1            c2            c3            c4            c5
>    108     1     2     3     9
> ------------------------
>
>

This means that all relevant values are simply looked up in ffbonded.itp.

-Justin

> Any idea of what could be happening?
>
> Best wishes,
>
> Rebeca.
>
> Dr. Rebeca Garcia
> Santiago de Compostela University
> Spain
>   		 	   		
>

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

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

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