[gmx-users] which version it is

[Thomas Piggot]

Hi Stephane,

The confusion was my fault, I did not realise that there were newly 
developed CHARMM36 protein parameters (Justin kindly pointed this out). 
You were quite correct that the contribution only contains the update 
for the lipids.

Cheers

Tom

On 19/11/12 18:49, ABEL Stephane 175950 wrote:
> 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.ABEL at cea.fr>
> Subject: [gmx-users] which version it is
> To: "gmx-users at gromacs.org" <gmx-users at gromacs.org>
> Message-ID:
>          <3E39B768BB199548AB18F7289E7534AF02D1CE1A at 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.piggot at soton.ac.uk>
> Subject: Re: [gmx-users] which version it is
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <50AA5E2C.4000206 at 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 <jalemkul at vt.edu>
> Subject: Re: [gmx-users] which version it is
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <50AA5F94.6090208 at 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.piggot at soton.ac.uk>
> Subject: Re: [gmx-users] which version it is
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <50AA62DB.8010408 at 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.
>
>
>

-- 
Dr Thomas Piggot
University of Southampton, UK.