[gmx-users] charmm c36 lipids
t.piggot at soton.ac.uk
Fri Oct 1 15:02:02 CEST 2010
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.
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:
> 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 I've put it on the old (and outdated) port homepage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>.
> 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,
>> Dr.-Ing. Sven Jakobtorweihen
>> Hamburg University of Technology
>> Institute of Chemical Reaction Engineering / V2
>> Eissendorfer Str. 38
>> 21073 Hamburg
>> 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.
>>> Drew Bennett
Dr Thomas Piggot
University of Southampton, UK.
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