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
Cheers
Tom
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distribution have outdated CHARMM22+CMAP parameters for proteins and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.
--
Gromacs Users mailing list
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a
mail to gmx-users-requ...@gromacs.org.
