[gmx-users] Parametrisation of the heteroatomic pdb
Justin A. Lemkul
jalemkul at vt.edu
Wed Nov 9 21:09:46 CET 2011
James Starlight wrote:
> 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
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
> 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?
> 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 ?
> At this point, please start a new thread for your questions, as
> these topics are completely unrelated to where you started.
> 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
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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