James,
> 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.
ok but the principle is the same...
> 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.
So here your best bet might be to use a text editor such as "gedit" to
select the wanted residues in the PDB file and save a new PDB file for
these selected residues. Then, load this new PDB file in XLEaP;
visualization will be far more simplified...
You could also write a script to save all the atoms within X angstroms
of a specified atom if you want to save several non-consecutive
residues - mine is quite basic :-)
Then, you could load these selected residues in XLEaP to perform the
structural modifications you need or you could run Ante_R.E.D. 2.0 at
R.E.D. Server to generate a Java Applet for your PDB file so that you
can directly work with Jmol on this PDB file...
See
http://q4md-forcefieldtools.org/REDS/faq.php#19
+
http://q4md-forcefieldtools.org/REDS/faq.php#20
> 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).
See above.
> 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.
I think in your case, a script, a text editor and XLEaP and/or Jmol
should do the job ;-)
regards, Francois
> 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
>>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sat Jan 28 2012 - 09:30:02 PST
