[gmx-users] charmm c36 lipids

Nicolas SAPAY nicolas.sapay at cermav.cnrs.fr
Fri Oct 1 16:17:45 CEST 2010


I also had the opportunity to import and test the CHARMM36 lipids with
Gromacs. There is not particular issue with those lipids and I guess any
script able to convert charmm27 topology and parameter files in Gromacs
file should work with charmm36.


> Hi Par,
> I have a working version of the CHARMM36 lipids that I converted myself,
> which I am fairly confident is correct. I shall check your parameters
> against my ones to confirm everything is the same and report back to the
> list. I don't see anything which would not work for your script as there
> are not any major changes to the forcefield in CHARMM36.
> Cheers
> Tom
> Pär Bjelkmar wrote:
>> Hello Sven, Drew and gmx-users,
>> I've gotten requests from users that want to use the c36 CHARMM lipids
>> in GROMACS (see below). So I answer both of you and the rest of the
>> community in this e-mail.
>> I have a script that parses the top and par files of CHARMM force
>> field(s). It's not the most general piece of code there is so it will
>> not be able to convert files that do not follow the format the CHARMM
>> top and par files had when I wrote it (version c32b1). Also, it cannot
>> parse the toppar files (i.e. what's called the toppar stream files in
>> CHARMM). I downloaded the force field from:
>> http://mackerell.umaryland.edu/download.php?filename=CHARMM_ff_params_files/toppar_lipid_all36.tgz
>> My script is able to parse the top_lipid_all36.rtf and
>> par_all36_lipid.prm files without any errors and generate the
>> corresponding GROMACS rtp, atp, bonded and nonbonded files. I'm not an
>> CHARMM expert but if they haven't changed the force field considerable
>> lately (by changing parameter definitions and functional forms of the
>> force field for example) the files generated by the script should be the
>> correct GROMACS translation. However, I cannot guarantee that all went
>> well so I would suggest that those of you who are interested in this
>> look through the files and convince yourself that the script did the job
>> before running production runs with these parameters.
>> I've put it on the old (and outdated) port homepage
>> (http://www.dbb.su.se/User:Bjelkmar/Ffcharmm) so that those of you who
>> are interested in this can access and test it. If nothing seems to be
>> wrong after some of you have tested it I'm going to add it to the user
>> contributions on gromacs.org <http://gromacs.org>.
>> Regards,
>> Pär Bjelkmar
>> 1 okt 2010 kl. 09.53 skrev Sven Jakobtorweihen:
>>> Dear Pär Bjelkmar,
>>> thanks for implementing the CHARMM force field into GROMACS, that is
>>> really useful. Recently the CHARMM developers have introduced an
>>> updated lipid force field CHARMM36 for lipids, see Klauda et al. J.
>>> Phys. Chem. B, 2010, 114, 7830 (doi: 10.1021/jp101759q). It seems that
>>> this is an important improvement over the preceding version. I checked
>>> gromacs version 4.5.1 and the git-repository; unfortunately, the
>>> charmm36 lipids are not yet available in gromacs. However, I could
>>> write some scripts to convert the charmm files to gromacs files, I
>>> have the feeling the bonded parameter conversion is straight forward
>>> (having the charmm27 files for gromacs), but I fear that transferring
>>> the bonded parameters is tedious. So my question is: Do you have by
>>> any change already gromacs files for charmm36 lipids? Or are scripts
>>> available to convert charmm FF to gromacs FF files? I am aware of the
>>> charmm_to_gromacs perl scripts on the gromacs website. But as fare as
>>> I know they are not compatible with the official implementation of
>>> charmm in gromacs, or am I wrong?
>>> Thanks for your help.
>>> Best regards,
>>> Sven
>>> --
>>> *****************************************
>>> Dr.-Ing. Sven Jakobtorweihen
>>> Hamburg University of Technology
>>> Institute of Chemical Reaction Engineering / V2
>>> Eissendorfer Str. 38
>>> 21073 Hamburg
>>> Germany
>>> PHONE : ++49 (0) 40 42878 2491
>>> FAX   : ++49 (0) 40 42878 2145
>>> E-MAIL: jakobtorweihen at tuhh.de <mailto:jakobtorweihen at tuhh.de>
>>> *****************************************
>>> 3 sep 2010 kl. 20.56 skrev Drew Bennett:
>>>> Dear Pr Bjelkmar,
>>>> I saw on the gromacs mailing list that you have python a script for
>>>> converting CHARMM ff to GMX.
>>>> I would greatly appreciate if you could please send it to me.
>>>> I am trying to use the new CHARMM36 lipids for a simulation with a
>>>> membrane protein.
>>>> Thank-you.
>>>> Drew Bennett
> --
> Dr Thomas Piggot
> University of Southampton, UK.
> --
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[ Nicolas Sapay - Post-Doctoral Fellow ]
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