[gmx-users] D- &/or L- cmap for charmm36 (gromacs.org_gmx-users Digest, Vol 149, Issue 71)

[Justin Lemkul]

On 10/4/16 2:00 AM, HENRY WITTLER wrote:
>
> Thanks, for the previous reply.
>
> Will the CHARMM cmap and topology for D-amino acids be included in gmx for a later version of gmx charmm36? It doesn't seem straightforward to convert the charmm D-aa cmap parameters to gmx cmap.itp format. Can this program be used for this 'cgenff_charmm2gmx.py' at http://mackerell.umaryland.edu/charmm_ff.shtml#charmm
>

I will consider putting it in.  Note that we have an update to the CHARMM36 
protein parameters (specifically CMAP) that is about to be published, so no 
update will be posted until then (though the files, in CHARMM format, are 
available, but we're waiting on the conversion until the reference is 
available).  The D-amino acid CMAP, however, has not been adjusted, but can 
easily be converted.

In the meantime, you can certainly proceed with the existing files.  The CMAP 
conversion is just converting energy units.  And a new DSER entry would just 
require changing the CA type in the existing SER .rtp entry to create a new residue.

-Justin

>
> Cheers,
> Henry Wittler
>
> Phd in Molecular modelling group (Brian J. Smith)
> Department of Chemistry and Physics, La Trobe Institute for Molecular Science, La Trobe University, Victoria 3086, Australia
> Tel: 0432901627
>
>
>
> Message: 3
> Date: Wed, 21 Sep 2016 15:08:23 -0400
> From: Justin Lemkul <jalemkul at vt.edu>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] D- &/or L- cmap for charmm36
> Message-ID: <5156078a-2572-401b-ec29-62dd5ae8bb6f at vt.edu>
> Content-Type: text/plain; charset=windows-1252; format=flowed
>
>
>
> On 9/21/16 1:43 AM, HENRY WITTLER wrote:
>> Greetings.
>>
>>
>> If anyone can give insight please.
>>
>>
>> I want to do a MD for insulin a 51aa protein, mutating one residue from L to D-Ser.
>>
>> I have runned 1.5us for the L- Ser (with cmap), and want to repeat it for the D-Ser, with gmx v.5.0.4 charmm36 mars14 version.
>>
>>
>> It seems in the traditional CHARMM one have to change dihedrals involved with changing L- to D- (http://www.ks.uiuc.edu/Training/Tutorials/science/topology/topology-html/node4.html), also the cmap is for L-aa (http://mackerell.umaryland.edu/~kenno/cgenff/faq.php<http://mackerell.umaryland.edu/%7Ekenno/cgenff/faq.php>).
>>
>>
>> In link http://www.swisssidechain.ch/D_residues.php gives topology D-aa for gmx-charmm, without changing anything about cmap.itp, only .hdb and .rtp.
>>
>>
>> Previous discussions (http://gromacs.org_gmx-users.maillist.sys.kth.narkive.com/r1t0ZqeF/converting-l-to-d-amino-acid-in-the-charmm-force-field-in-gromacs-where-to-alter-dihedral) and my own testing MD and looking at it in vmd etc, seems to imply that the .top, .itp do not distinguish about chirality, is this the case?
>>
>> How is cmap.itp implemented in gmx, is these parameters for L-, and D- aminoacids?
>>
>
> The parameters provided are for L-amino acids.  There are D-amino acid CMAP
> parameters available in CHARMM, but not in GROMACS format.  See the latest force
> field distribution on http://mackerell.umaryland.edu/charmm_ff.shtml#charmm and
> look in stream/prot/toppar_all36_prot_d_aminoacids.str
>
> The D vs L stereochemistry is made possible by assigning a special atom type to
> the CA atom (CTD1 instead of CT1) so you can apply residue-specific parameters.
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul<http://mackerell.umaryland.edu/%7Ejalemkul>
>

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==================================================