[gmx-users] Parametrisation of the heteroatomic pdb

[James Starlight]

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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