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 Fri Jan 27 2012 - 23:30:02 PST
