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.
Sincerely,
On Thu, May 28, 2009 at 12:38 AM, Ross Walker <ross.rosswalker.co.uk> wrote:
> 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.ambermd.org [mailto:amber-bounces.ambermd.org] On
> > Behalf Of manoj singh
> > Sent: Wednesday, May 27, 2009 8:48 PM
> > To: amber.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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> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
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Received on Fri May 29 2009 - 01:11:20 PDT
