[gmx-users] errors with charmm36 ?

Justin Lemkul jalemkul at vt.edu
Tue Jan 14 17:16:20 CET 2014

On 1/14/14, 10:58 AM, hubert santuz wrote:
> I use this charmm36
> (http://www.gromacs.org/@api/deki/files/184/=charmm36.ff_4.5.4_ref.tgz, from
> Piggot et al, 2012, JCTC) which have slight differences in the order and in the
> name of few atoms compared to the one you used.
> So, everything I said concern only this version ;)

I think it is probably worth emphasizing a point I have made previously, because 
I suspect there may be some confusion among the users out there.  The tarball 
that can be downloaded from the website contains updated parameters for CHARMM36 
lipids ONLY.  The parameters in that distribution have outdated CHARMM22+CMAP 
parameters for proteins and CHARMM27 for nucleic acids (i.e. the files 
distributed as "charmm27.ff" in Gromacs).  Users should not be led to believe 
that this tarball contains the full CHARMM36 force field, which is a different 
entity, available only from the MacKerell lab (note we will be uploading a new 
tarball soon that has updated parameters for CGenFF 2b8).


> Cheers,
> Hubert
> Le 14/01/2014 16:42, Albert a écrit :
>> On 01/14/2014 04:12 PM, Justin Lemkul wrote:
>>> The .top is what matters, and your topology showed a clearly different order
>>> of atoms.  Check the correspondence of the output configuration from pdb2gmx
>>> and the .top file.  Inputs and .rtp entries are irrelevant once pdb2gmx is
>>> done working.
>>> -Justin
>> Hi Justin:
>> Many thanks for your helpful advices. The problem solved now. I some kind of
>> mix the old c36 FF with the new one. I just update it in my system few days ago.
>> thanks again for sugguestions.
>> best
>> Albert


Justin A. Lemkul, Ph.D.
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


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