[gmx-users] Parametrisation of the heteroatomic pdb

James Starlight jmsstarlight at gmail.com
Thu Nov 10 09:05:44 CET 2011


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?

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


James

2011/11/9 Justin A. Lemkul <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<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>>
>>
>>
>>
>>
>>    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> | (540) 231-9080
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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 | (540) 231-9080
> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>
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