[gmx-users] Parametrisation of the heteroatomic pdb

[Mark Abraham]

On 10/11/2011 7:05 PM, James Starlight wrote:
> Justin,
>
>
> I've also look for the cap editing in the pymol but it seems that that 
> function lacks in that program
>
> By the way, what are specificity of such Cap groups ? Do they are only 
> sheld charges on the termi or have something addition function?

They can. The purpose of a simulation is to provide a model of reality. 
How one would wish to cap a peptide depends what is being modelled under 
what conditions with what objectives in mind.

>
> What difference beetwen different caps I cant understand why in my 
> structure there are so non-standart groups.

Shrug. We don't even know what they are... Wherever you sourced your 
starting structure should discuss how and why the termini have such caps.

Mark

>
>
> James
>
> 2011/11/9 Justin A. Lemkul <jalemkul at vt.edu <mailto:jalemkul at vt.edu>>
>
>
>
>     James Starlight wrote:
>
>         Justin,
>
>         Could you tell me another alternative ways to replace existing
>         cap groups in my pdb besides xleap ? ( I've had  many problems
>         with the pdb's processed by this soft). Also I've tried to
>         make topology for the non-standart caps by PRODRG but I also
>         have some problems with such parametrisation.
>
>
>     Unless you describe your problems, there's very little anyone can
>     or will try to do to help you.  I've never had a problem with an
>     xleap coordinate file, so I can't offer you any additional
>     guidance with that.  Otherwise, there are dozens of programs that
>     are capable of drawing molecules or editing files.  See, for instance:
>
>     http://www.gromacs.org/Documentation/File_Formats/Coordinate_File#Sources
>
>     -Justin
>
>
>         Also I've not found suitable topology for some D-isomers (
>         it's strange that parametriation for such typical non-standart
>         residues is absent in all force fields ). As I understood I
>         cant use topology of L-analogs for the parametrisation of such
>         D-forms because I dont know suitable parameters for dihedrals
>         for instance.
>         Have someone pre-built parameters for the D-aa for Gromos or
>         Charmm force field?
>
>
>         Thanks,
>
>         James
>
>         2011/10/29 Justin A. Lemkul <jalemkul at vt.edu
>         <mailto:jalemkul at vt.edu> <mailto:jalemkul at vt.edu
>         <mailto:jalemkul at vt.edu>>>
>
>
>
>
>            James Starlight wrote:
>
>                Justin, hello!
>
>                Could you tell me what exactly program from the Amber tools
>                package you've used for the KALP peptide preparation
>         e.g for
>                capping ?
>
>
>            xleap
>
>            At this point, please start a new thread for your questions, as
>            these topics are completely unrelated to where you started.
>
>            -Justin
>
>
>            --     ==============================__==========
>
>
>            Justin A. Lemkul
>            Ph.D. Candidate
>            ICTAS Doctoral Scholar
>            MILES-IGERT Trainee
>            Department of Biochemistry
>            Virginia Tech
>            Blacksburg, VA
>            jalemkul[at]vt.edu <http://vt.edu> <http://vt.edu> | (540)
>         231-9080
>         http://www.bevanlab.biochem.__vt.edu/Pages/Personal/justin
>         <http://vt.edu/Pages/Personal/justin>
>         <http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>
>            ==============================__==========
>            --     gmx-users mailing list gmx-users at gromacs.org
>         <mailto:gmx-users at gromacs.org>
>         <mailto:gmx-users at gromacs.org <mailto:gmx-users at gromacs.org>>
>         http://lists.gromacs.org/__mailman/listinfo/gmx-users
>
>         <http://lists.gromacs.org/mailman/listinfo/gmx-users>
>            Please search the archive at
>         http://www.gromacs.org/__Support/Mailing_Lists/Search
>
>         <http://www.gromacs.org/Support/Mailing_Lists/Search> before
>         posting!
>            Please don't post (un)subscribe requests to the list. Use
>         the www
>            interface or send it to gmx-users-request at gromacs.org
>         <mailto:gmx-users-request at gromacs.org>
>         <mailto:gmx-users-request at gromacs.org
>         <mailto:gmx-users-request at gromacs.org>>.
>            Can't post? Read http://www.gromacs.org/__Support/Mailing_Lists
>         <http://www.gromacs.org/Support/Mailing_Lists>
>
>
>
>     -- 
>     ========================================
>
>     Justin A. Lemkul
>     Ph.D. Candidate
>     ICTAS Doctoral Scholar
>     MILES-IGERT Trainee
>     Department of Biochemistry
>     Virginia Tech
>     Blacksburg, VA
>     jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
>     http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
>     ========================================
>     -- 
>     gmx-users mailing list gmx-users at gromacs.org
>     <mailto:gmx-users at gromacs.org>
>     http://lists.gromacs.org/mailman/listinfo/gmx-users
>     Please search the archive at
>     http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>     Please don't post (un)subscribe requests to the list. Use the www
>     interface or send it to gmx-users-request at gromacs.org
>     <mailto:gmx-users-request at gromacs.org>.
>     Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
>
>
>

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20111110/ed232949/attachment.html>