Thanks!!
I have downloaded the ".prep" file for ATP from the site as you mentioned. I also tried to load ".prep" file to generate the corresponding topology file and coordinate file. I used "loadAmberPrep" to load the "prep" file as mentioned in AmberTools. But I failed to do this. Some how the "loadAmberprep" command is not working properly.
If you kindly mention the steps how to load a ".prep" file and generate the topology file and coordinat file from this, it will be very helpful for me.
With my best regards
Sindrila
From: David A. Case <case.biomaps.rutgers.edu>
To: Sindrila Dutta banik <sindrila.duttabanik.yahoo.com>; AMBER Mailing List <amber.ambermd.org>
Sent: Thursday, 9 June 2011 10:25 PM
Subject: Re: [AMBER] Problem related to teh residue template and add ion
On Thu, Jun 09, 2011, Sindrila Dutta banik wrote:
>
> I want to study the dynamics of a enzyme complesed with the substrate
> molecules. In my case one of teh substrate molecule is ATP.
>
> The crystal structure contains the ATP but the residue name is as
> "HETATOM".
The residue name is a three character (at most) name in columns 18-20 of
the ATOM or HETATM record. The residue name is not "HETATM".
> But for ATP what is the residue template.
Please see
http://www.pharmacy.manchester.ac.uk/bryce/amber.
> I also want to add ion in a particular position. How to do this?
This question is hard to understand. By "ion" do you mean the ATP, or some
other ion? The ATP would automatically be placed where it is in the crystal
structure. If you want some other position, or some other ion, that would be
a model building or docking problem, which is ordinarily outside the scope
of the Amber suite of programs. But it may well be that I don't understand
what you want to do....
....dac
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Received on Fri Jun 10 2011 - 08:30:03 PDT
