[gmx-users] Parametrisation of the heteroatomic pdb

[James Starlight]

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.


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>

>
>
> 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
>
>
> --
> ==============================**==========
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> Justin A. Lemkul
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> 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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