Dear all!
Fistly, many thanks for the so detailed advises for my problem.
Fistly recently I've already used Xleap just for adding CAP groups to my
peptide and subsequent relaxation of the selection :)
This was quite simple because of small size of that peptide.
But Now I have quite big protein where I want to perform some point
mutation to study further stability of that protein. One of wich is the
non-standart cyclisation of the adjacent atoms :) So I just need to find
desired motif and create one covalent bond.
Firstly I'm looking for the simplest way to do it.
As I understood the bonds are predifened in the topology so some
topology-editngs servers like PRORG or RED can operate with the ISOLATED
motiv wich will need further back insertion to the protein. I suppose that
its very dificult for such trivial operation like creation of one bond :))
As I've wrote I've loaded my pdb in the Xleap but I cant find SEQUENCE
SEARCH in EDITING mode of the xleap ( the protein too large so its very
difficult to find my motif visualy).
By the way could you also advise me some another software for easy pdb
editing? I've heard that MODDELER or MAESTRO software are very suitable for
that.
Thanks again,
James
2012/1/28 FyD <fyd.q4md-forcefieldtools.org>
> Dear James,
>
> > I need to edit my pdb structure for further MD simulation.
> > 0- I've successful load my structure in the Xleap and run EDIT mode.
> > 1- I need to find special triplet motif ( e.g Thr-Leu-Gly) in my big
> protein.
> > 2- In this motiv I want to create new Covalent bond between 2 adjacent
> > atoms ( e.g N atom in Gly and C atom in Thr) ( distance 1 A) and than
> > make geometry optimisation of this new motif.
> >
> > How I could make it in Xleap?
>
> You first need to create a new _whole_ molecule i.e. in general an
> amino-acid based structure capped by the ACE & NME chemical groups.
> See http://q4md-forcefieldtools.org/Tutorial/Tutorial-1.php#10
> You can indeed use XLEaP for building the PDB file of your modified
> residue. Once you know how to use XLEaP it is very powerful (I build
> most of the modified structures I need using XLEaP starting from
> available libraries); However, the differences between 'Build'/'Add H
> & Build' and 'Relax selection' are not that obvious, when one first
> starts. Loading a force field and defining the atom types for the
> molecule part to be relaxed help to get the target geometry. You need
> to spend some time here (difficult to help by email)...
>
> You might also decide to use Jmol/Java applet in R.E.D. Server to
> create this _whole_ molecule in the PDB file format. You can drag &
> optimize a chemical group in your Java applet, and this makes the
> construction of cyclic structure quite efficient... Here, you have to
> learn how to use Jmol & spend some time once again...
> See http://q4md-forcefieldtools.org/REDS/faq.php#20
>
> ---
>
> Then, in a second step from this PDB file you will have to generate a
> force field library for a _fragment_ generated from the whole molecule
> previously obtained.
> See http://q4md-forcefieldtools.org/Tutorial/Tutorial-1.php#1
> http://q4md-forcefieldtools.org/Tutorial/Tutorial-3.php#1
> & then
> http://q4md-forcefieldtools.org/Tutorial/Tutorial-1.php#10
> http://q4md-forcefieldtools.org/Tutorial/Tutorial-3.php#24
> Procedures are now automatized in R.E.D. server, and/or you can also
> use the standalone version of the R.E.D. program.
> See http://q4md-forcefieldtools.org/REDS/
> http://q4md-forcefieldtools.org/RED/
>
> If you need more help you should provide a drawing of your modified
> structure so that we can more easily assist you.
>
> regards, Francois
>
>
>
>
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Received on Sat Jan 28 2012 - 01:00:02 PST
