Hi Thomas and Justin,
I agree with you, but I think that Albert asked if the GROMACS 4.5.4 version of
the CHARMM36 force field files contain the newly developed parameters for
protein (also called CHARMM36) and described in
Best, R. B., Zhu, X., Shim, J., Lopes, P. E. M., Mittal, J., Feig, M., &
MacKerell, A. D. (2012). Optimization of the additive CHARMM all-atom protein force
field targeting improved sampling of the backbone φ, ψ and side-chain χ1 and χ2
dihedral angles. Journal of Chemical Theory and Computation, 120718184839007.
doi:10.1021/ct300400x
I said no
Sorry if it was not clear in my previous message
Stephane
----------------------------------------------------------------------
Message: 1
Date: Mon, 19 Nov 2012 16:14:48 +0000
From: ABEL Stephane 175950 <stephane.a...@cea.fr>
Subject: [gmx-users] which version it is
To: "gmx-users@gromacs.org" <gmx-users@gromacs.org>
Message-ID:
<3e39b768bb199548ab18f7289e7534af02d1c...@exdag0-b0.intra.cea.fr>
Content-Type: text/plain; charset="us-ascii"
Hi,
Probably the "CHARMM27_protein+Charmm36_lipids" version. AFAIK, the second
version was not already converted in GROMACS format.
Stephane
---------------------------------------------------
hello:
I found a charmm36.tar.gz in Gromacs website
GROMACS 4.5.4 version of the CHARMM36 force field files. These updated
CHARMM lipids allow the all-atom simulations of membrane and
membrane-protein systems without the use of surface tension. Check out
the forcefield.doc for more information regarding these files
71.65 kB 15:42, 25 Sep 2012 TomPiggot
I am just wondering, is the the one with
CHARMM27_protein+Charmm36_lipids or it is CHARMM36_protein+CHARMM36_lipids?
thank you very much
best
Albert
------------------------------
Message: 3
Date: Mon, 19 Nov 2012 16:28:28 +0000
From: Thomas Piggot <t.pig...@soton.ac.uk>
Subject: Re: [gmx-users] which version it is
To: Discussion list for GROMACS users <gmx-users@gromacs.org>
Message-ID: <50aa5e2c.4000...@soton.ac.uk>
Content-Type: text/plain; charset="ISO-8859-1"; format=flowed
Hi,
As I understand it, the current and most up to date CHARMM protein force
field (as included in both the charmm27 and charmm36 force field
directories) is the CHARMM22 protein force field with the CMAP
correction. In other words there would be no difference between the two
options originally mentioned.
Cheers
Tom
ABEL Stephane 175950 wrote:
Hi,
Probably the "CHARMM27_protein+Charmm36_lipids" version. AFAIK, the second
version was not already converted in GROMACS format.
Stephane
---------------------------------------------------
hello:
I found a charmm36.tar.gz in Gromacs website
GROMACS 4.5.4 version of the CHARMM36 force field files. These updated
CHARMM lipids allow the all-atom simulations of membrane and
membrane-protein systems without the use of surface tension. Check out
the forcefield.doc for more information regarding these files
71.65 kB 15:42, 25 Sep 2012 TomPiggot
I am just wondering, is the the one with
CHARMM27_protein+Charmm36_lipids or it is CHARMM36_protein+CHARMM36_lipids?
thank you very much
best
Albert
--
Dr Thomas Piggot
University of Southampton, UK.
------------------------------
Message: 4
Date: Mon, 19 Nov 2012 11:34:28 -0500
From: Justin Lemkul <jalem...@vt.edu>
Subject: Re: [gmx-users] which version it is
To: Discussion list for GROMACS users <gmx-users@gromacs.org>
Message-ID: <50aa5f94.6090...@vt.edu>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
On 11/19/12 11:28 AM, Thomas Piggot wrote:
Hi,
As I understand it, the current and most up to date CHARMM protein force field
(as included in both the charmm27 and charmm36 force field directories) is the
CHARMM22 protein force field with the CMAP correction. In other words there
would be no difference between the two options originally mentioned.
There is indeed a CHARMM36 protein force field that is distinct from the one
included in CHARMM27 (which is, as you say, CHARMM22 + CMAP).
http://www.charmm.org/ubbthreads/ubbthreads.php?ubb=showflat&Number=30472
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
------------------------------
Message: 5
Date: Mon, 19 Nov 2012 16:48:27 +0000
From: Thomas Piggot <t.pig...@soton.ac.uk>
Subject: Re: [gmx-users] which version it is
To: Discussion list for GROMACS users <gmx-users@gromacs.org>
Message-ID: <50aa62db.8010...@soton.ac.uk>
Content-Type: text/plain; charset="ISO-8859-1"; format=flowed
I must have missed that one, thanks for the link!
So, to confirm, the protein force field in the CHARMM36 force field
contribution is the CHARMM22 protein force field with the CMAP
correction. The contribution is just for the updated CHARMM36 lipids.
Cheers
Tom
Justin Lemkul wrote:
On 11/19/12 11:28 AM, Thomas Piggot wrote:
Hi,
As I understand it, the current and most up to date CHARMM protein
force field
(as included in both the charmm27 and charmm36 force field
directories) is the
CHARMM22 protein force field with the CMAP correction. In other words
there
would be no difference between the two options originally mentioned.
There is indeed a CHARMM36 protein force field that is distinct from the
one included in CHARMM27 (which is, as you say, CHARMM22 + CMAP).
http://www.charmm.org/ubbthreads/ubbthreads.php?ubb=showflat&Number=30472
-Justin
--
Dr Thomas Piggot
University of Southampton, UK.
