Re: [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 <jalem...@vt.edu <mailto:jalem...@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 <jalem...@vt.edu
        <mailto:jalem...@vt.edu> <mailto:jalem...@vt.edu
        <mailto:jalem...@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>

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

    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

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