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
-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 <jalem...@vt.edu <mailto:jalem...@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
http://www.bevanlab.biochem.__vt.edu/Pages/Personal/justin
<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
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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
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