Re: [AMBER] Building a new structure!

From: Ibrahim Said <saidibrahim569.gmail.com>
Date: Wed, 13 Feb 2013 10:37:50 +0200

Dear Francois
I have built my dipeptide (Lysine-fructose). and I used RESP ESP charge
derived server to assign the atomic charges. Please, I used xleap to add
the same fructose moiety to the lysine residue in my protein and added the
charges and atom types to this fructose part manually. Of course, I loaded
both of leaprc.ff99SB and Glycam_06h. Now I get both top and crd files but
I do not know if these steps are Ok or no. please can you help me.
Regards, Ibrahim


On Thu, Jan 24, 2013 at 9:51 AM, FyD <fyd.q4md-forcefieldtools.org> wrote:

> Dear Ibrahim,
>
> > I am trying to simulate the Schiff base for my protein in which
> > lysine is binding the fructose molecule through a covalent bond NZ-C1 of
> > fructose. Can I use xleap to build this structure and how. What I have in
> > my hand that I should separate lysine residue from the protein and attach
> > it to fructose and then re-ligate, is it correct. I do not know how can
> > xleap can do.
>
> If I understand you you are interested in constructing a new residue
> i.e. a L-lysine connected to D-fructose through an imine bond.
>
> You can use R.E.D. and/or R.E.D. Server for this work; and you can
> directly build a new central fragment for this new Lysine residue.
> See for instance: http://q4md-forcefieldtools.org/Tutorial/Tutorial-3.php
> &
> http://q4md-forcefieldtools.org/Tutorial/Tutorial-3.php#24
> vs
> http://q4md-forcefieldtools.org/Tutorial/Tutorial-3.php#25
>
> You could also consider splitting this 'lys-fructose' residue into two
> building blocks. You can find examples of such an approach in R.E.DD.B.
> See for instance in the sugar domain:
> http://q4md-forcefieldtools.org/REDDB/projects/F-85/
> http://q4md-forcefieldtools.org/REDDB/projects/F-72/
> http://q4md-forcefieldtools.org/REDDB/projects/F-71/
>
> R.E.D. uses the P2N file format as input described at:
> http://q4md-forcefieldtools.org/Tutorial/Tutorial-1.php#3
> & generates FF library in the mol2 file format described at:
> http://q4md-forcefieldtools.org/Tutorial/leap-mol2.php
> This mol2 file format is directly usable in the LEaP prgram as described
> at:
> http://q4md-forcefieldtools.org/Tutorial/Tutorial-1.php#1
>
> regards, Francois
>
>
>
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Received on Wed Feb 13 2013 - 01:00:03 PST