[gmx-users] problem with Charmm36 ff

Wed Jun 18 18:45:51 CEST 2014

Thank you very much, Justin and Thomas, for your helpful effort!!!
Best Regards

> 
> 
> On 6/18/14, 11:45 AM, Thomas Piggot wrote:
> > Apologies for any confusion over the naming of the downloadable 
files, they were
> > originally made well before any modification to the protein 
parameters were
> > published. Due to the way the CHARMM27 force field was named 
"charmm27.ff" but
> > also included things you probably shouldn't call CHARMM27, like the 
protein
> > force field which is (as you mentioned) CHARMM22 + CMAP, it made 
sense at the
> > time to just call the force field "charmm36.ff".
> >
> > Anyway, I have just updated the description of the downloadable 
force field (on
> > the user contribution section of the website) to make it clearer 
that it
> > includes CHARMM36 for the lipids and CHARMM22 + CMAP for the 
protein. Hopefully
> > this will alleviate any future confusion for people.
> >
> 
> Thanks, Tom.  Much appreciated.  The CHARMM27 issue is another good 
one. 
> Technically C27 is a nucleic acid force field, so it always gets a 
chuckle when 
> people publish proteins "simulated with C27." ;)
> 
> -Justin
> 
> > Cheers
> >
> > Tom
> >
> > On 18/06/14 16:19, Justin Lemkul wrote:
> >>
> >>
> >> On 6/18/14, 11:03 AM, Esteban.Pedrueza at uv.es wrote:
> >>> 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
> >>>
> >>
> >> The problem is in the implementation of the force field, not 
necessarily the
> >> force field itself.  The C36 lipid parameters were developed 
alongside the
> >> C22/CMAP implementation of proteins, and then later those C22/CMAP 
parameters
> >> were further refined to yield the C36 protein force field.  The 
atomtypes
> >> implemented in the Gromacs version of C22/CMAP (under the 
charmm27.ff
> >> directory) are named differently than the atomtypes in the C36 
force field
> >> (which we take directly from CHARMM).  There is a hybrid C22/CMAP + 
C36 force
> >> field available on the Gromacs downloads page that could rectify 
this
> >> situation, but it is misleadingly named "CHARMM36," but in fact it 
is only C36
> >> lipids.
> >>
> >> In either case, we consider the C36 protein parameters superior to 
C22/CMAP,
> >> but for the purposes of reproducing existing work I can understand 
why the
> >> combination might still be useful.
> >>
> >> -Justin
> >>
> >>>>
> >>>>
> >>>> 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
> >>>>
> >>>> ==================================================
> >>>> --
> >>>> Gromacs Users mailing list
> >>>>
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> >>> posting!
> >>>>
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> >>>>
> >>>
> >>>
> >>> --
> >>> ********************************
> >>> Esteban Pedrueza Villalmanzo
> >>> e-mails:
> >>> esteban.pedrueza at uv.es
> >>> espevi1982 at hotmail.com
> >>> ********************************
> >>>
> >>>
> >>>
> >>
> >
> 
> -- 
> ==================================================
> 
> 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
********************************