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

[HENRY WITTLER]

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


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>