[gmx-users] Parametrisation of the heteroatomic pdb

James Starlight jmsstarlight at gmail.com
Wed Nov 9 20:56:47 CET 2011


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

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



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
> --
> ==============================**==========
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> 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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