[gmx-users] problem with Charmm36 ff
Justin Lemkul
jalemkul at vt.edu
Wed Jun 18 17:49:54 CEST 2014
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 originally made well before any modification to the protein parameters were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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>>>
>>>
>>> --
>>> ********************************
>>> 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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