[gmx-users] problem with Charmm36 ff

[Esteban.Pedrueza at uv.es]

Thanks, Justin.
I will do it right now but, in the meantime, what do you think about the 
paper I mention? They use C36 for lipids an C22 for melittin, as I 
understand well. I am aware that they dont use Gromacs. If it is 
published that this ff "mix" works well... Maybe there is something I 
miss.
Thank you very much again

> 
> 
> 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
> 
> ==================================================
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--
********************************
Esteban Pedrueza Villalmanzo
e-mails:
esteban.pedrueza at uv.es
espevi1982 at hotmail.com
********************************