[gmx-users] problem with Charmm36 ff

[Justin Lemkul]

On 6/18/14, 10:25 AM, Esteban.Pedrueza at uv.es wrote:
> Dear gmx users,
> I am trying to make MD for a DPPC bilayer with a melittin protein (pbd
> ID: 2MLT) positioned in the water slab, using Charmm36 ff for the lipids
> and Charmm22 for melittin, following this paper (Andersson, et all
> Biophysical Journal Volume 104 March 2013 L12–L14).  The procedure is
> the following:
> 1) I go to Klauda web page
> (http://terpconnect.umd.edu/~jbklauda/research/download.html) and
> download the DPPC bilayer (pdb file), eliminate the water and make:
> pdb2gmx -f bilayer.pdb -o bilayer.gro (choosing CHARMM36 all-atom force
> field, previously downloaded from charmm36-mar2014.ff from Charmm
> webpage, and tip3p water)
>
> 2)for the melittin: pdb2gmx -f 2MLT.pdb -o 2MLT.gro (choosing  CHARMM27
> all-atom force field (with CMAP) - version 2.0,  and tip3p water)
>
> I merged the 2 .gro's and solvated and it is OK. However, when I go to
> add ions with grompp, I obtain the following error:
>
> ------------------------------------------------------
> Program grompp, VERSION 4.6.5
> Source code file: /home/pedrueza/gromacs-4.6.5/src/kernel/toppush.c,
> line: 1336
>
> Fatal error:
> Atomtype HB not found
> For more information and tips for troubleshooting, please check the
> GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> -------------------------------------------------------
>
> My topol.top file is this: (previously I modified the topol.top files to
> itp simply erasing the #include "charmm27.ff/forcefield.itp" (2MLT) and
> #include "charmm36-mar2014.ff/forcefield.itp" (dppc), besides the
> [molecules], [system] and the other directives, like posre or ions .itp)
>
> -------------------------------------------
> ; Include forcefield parameters
> #include "charmm36-mar2014.ff/forcefield.itp"
>
> ; Include chain topologies
> #include "dppc.itp"
> #include "2MLT.itp"
>
> ; Include water topology
> #include "charmm36-mar2014.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 Position restraint file
> #ifdef POSRES
> #include "posre_dppc.itp"
> #endif
>
> ; Include Position restraint file
> #ifdef POSRES
> #include "posre_2MLT.itp"
> #endif
>
> ; Include topology for ions
> #include "charmm36-mar2014.ff/ions.itp"
>
> [ system ]
> ; Name
> DPPC bilayer plus 2MLT in water
>
> [ molecules ]
> ; Compound        #mols
> Other               72	
> Protein             1
> SOL              4054
> ---------------------------------------------------------------
>
> I think is a problem with nomenclature of atoms, but it is strange the
> mixing of the 2 forcefields???

Yes, it is.  Use CHARMM36 for everything.

-Justin

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

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

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

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

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