AMBER Archive (2009)

Subject: RE: [AMBER] Changing bond length

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Wed May 27 2009 - 23:38:59 CDT

Hi Manoj,

You might want to consider some kind of QM/MM for this in order to allow you
to simulate movement through actual transition states. However, if you
really just want to introduce a different bond constant for one residue then
you need to start by creating a non-standard residue. I suggest working
through some of the tutorials on the amber website to learn how to do this.

Start by creating a copy of the SER residue. E.g.

SEM = copy SER

The edit SEM in leap. Change the atom types for the bond you want to change
to atom types that are not currently in use. Note you may ultimately want to
calculate new charges for the transition state analogue as well.

Then save this residue. savemol2 SEM sem.lib

Next you need to create an frcmod file containing all the parameters for the
modified residue involving the new atom types - you can copy those you don't
want to change from the existing forcefield.

Then you modify your pdb file to rename the residue to be SEM.

Finally load leap.

Load the mol2 file,
Load the frcmod file
load the modified pdb

save your prmtop and inpcrd files.

Good luck,
Ross

> -----Original Message-----
> From: amber-bounces_at_ambermd.org [mailto:amber-bounces_at_ambermd.org] On
> Behalf Of manoj singh
> Sent: Wednesday, May 27, 2009 8:48 PM
> To: amber_at_ambermd.org
> Subject: [AMBER] Changing bond length
>
> Dear Amber users,
> In order to create a transition state analogue, I want to change
> the
> length of O-H bond of one particular Ser amino acid and bond length of
> O-H
> of one particular water molecule.
> I don't know how can I do this as I am new with Amber.
>
> I will be very thankful for any response regarding this.
>
> --
> _______________________________________________
> AMBER mailing list
> AMBER_at_ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber

_______________________________________________
AMBER mailing list
AMBER_at_ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber