AMBER Archive (2009)
Subject: Re: [AMBER] Changing bond length
From: manoj singh (mks.amber_at_gmail.com)
Date: Thu May 28 2009 - 12:00:14 CDT
Thanks for the reply and guidance.
Now, I want to derive the RESP charges for SER with custom O-H bond length.
I am not sure how can I do this as Gaussian will minimize the bond length to
its standard length.
On Thu, May 28, 2009 at 12:38 AM, Ross Walker <ross_at_rosswalker.co.uk> wrote:
> Hi Manoj,
> You might want to consider some kind of QM/MM for this in order to allow
> to simulate movement through actual transition states. However, if you
> really just want to introduce a different bond constant for one residue
> 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
> 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
> modified residue involving the new atom types - you can copy those you
> 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,
> > -----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.
> > --
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