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I've put it on the old (and outdated) port homepage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: [email protected] <mailto:[email protected]>
*****************************************
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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