On 10/11/2011 7:36 PM, James Starlight wrote:
Thanks Mark,
1) By the way do you know any database where I could obtain
information about function of the specific CAP groups ?
E.g as I know the most spread CAP on N is ACE group but in my case
there is For ( simple COH group) instead of ACE.
I think that parametrisation of such simple groups should not be very
complicate but it's strange that I've not found already built topology
for them.
People use acetyl rather than formyl cap either because that's what was
used in the experimental system, or because they are simulating a
fragment from a larger peptide and acetyl makes for a better model of a
peptide bond than formyl for only a small extra cost. I don't even know
that any force fields have parameters for H-C(O)-N(H)-R. I suggest you
use acetyl.
2) Also I've tried to made topology for D amoniacids. I've started
with the topology of L analogs e.g for D-val I've created enty based
on the Val in .rtp and .hdb files. Not I think I should to invert
impropers for the Calpha atoms that new topology represent to true
D-isomer :) But I'm not sure about how to make it correctly :)
In .itp I've found for new DVA residue
[ impropers ]
; ai aj ak al gromos type
N -C CA H gi_1
CA N C CB gi_2
CA CG1 CG2 CB gi_2
C CA +N O gi_1
here there are 2 enties for the Ca atoms. What should I do with it for
invertion?
First, identify that there's anything to invert. Look at the #define
lines for gi_1 and gi_2 and the manual sections for impropers. There's
nothing associated with any handedness. The impropers for chirality
prevent inversion, rather than enforcing a particular chirality. You can
test this yourself. Make a .tpr of an L-amino acid and .gro files of
each chirality, and then use mdrun -rerun Lconfiguration.gro -s
Lconfiguration and compare with mdrun -rerun Rconfiguration.gro -s
Lconfiguration.
Mark
James
2011/11/10 Mark Abraham <mark.abra...@anu.edu.au
<mailto:mark.abra...@anu.edu.au>>
On 10/11/2011 7:05 PM, James Starlight wrote:
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?
They can. The purpose of a simulation is to provide a model of
reality. How one would wish to cap a peptide depends what is being
modelled under what conditions with what objectives in mind.
What difference beetwen different caps I cant understand why in
my structure there are so non-standart groups.
Shrug. We don't even know what they are... Wherever you sourced
your starting structure should discuss how and why the termini
have such caps.
Mark
James
2011/11/9 Justin A. Lemkul <jalem...@vt.edu <mailto:jalem...@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
-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> <mailto: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
-- ==============================__==========
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Department of Biochemistry
Virginia Tech
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