[gmx-users] errors with charmm36 ?

Thomas Piggot t.piggot at soton.ac.uk
Tue Jan 14 18:21:35 CET 2014

I would just like to also re-iterate the point made by Justin. The 
conversion of the lipid parameters into GROMACS format was done before 
there were published updates to other parts of the CHARMM force field 
and so it is only the lipids which are the CHARMM36 parameters.

Regarding the choice of TIP3P water to use, further details regarding 
the impact of the water model upon lipid membranes (which can be large) 
and proteins (which was suggested to be minimal) can be seen in the 
following papers:

Lipids: http://pubs.acs.org/doi/abs/10.1021/ct3003157

Proteins: http://pubs.acs.org/doi/abs/10.1021/ct900549r



Justin Lemkul wrote:
> 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 distribution have outdated CHARMM22+CMAP parameters for proteins and 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).
> -Justin
>> 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

Dr Thomas Piggot
University of Southampton, UK.

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