AMBER Archive (2006)

Subject: Re: AMBER: Trouble with Leap

From: Ilyas Yildirim (yildirim_at_pas.rochester.edu)
Date: Thu Oct 19 2006 - 03:04:59 CDT

Dear Biswa,

I did not understand your question clearly. You have a big protein
structure and want to mutate some REGIONS of the protein, am I right? And
in those REGIONS, only some of the aminoacid residues are going to be
mutated, right?

Depending on which ver. of AMBER you are using, you can do this in 2
ways (as far as I know):

1. If it is AMBER 9 u are using, you can create the MUTATED aminoacid
residues seperately and using those residues, you can create the
prmtop/inpcrd files for the MUTATED structure. You will also create the
prmtop/inpcrd files for the unMUTATED structure. Using these files, you
can run sander and follow the Thermodynamic Integration Approach to get
the free energies of the transformation.

2. If it is AMBER 8, you can modify in Leap those residues which are
mutated, such that you will enter the names/types/charge differences for
each atoms in that residue (the perturbed parameters for those residues).
If you have created the mutated residues right, you will be able to create
inpcrd/prmtop file for your structure (using saveamberparmpert) which will
include the perturbation information in it. Using these inpcrd/prmtop
files, u can follow the TI Approach and get the free energy of this
particular transformation/mutation.

It is better if you follow Dave Case's tutorial. It will help u understand
how to edit the residues. Good luck.

Best,

PS: You should not edit all of the atoms in your structure, as it is not
logical to do. Just edit the mutated residues, save them in a library
file, and load them in Leap (which will enable Leap to use your modified
residue infromations).

On Thu, 19 Oct 2006, Biswa Ranjan Meher wrote:

>
> Dear Amber Users,
>
> I am doing FEP calculation for a protein system in an aqueous solution. I
> want to mutate some of the residues in the protein. For this I loaded the
> protein in xleap , selected all the atoms and through edit selected atoms
> from the unit editor menu bar created the spreadsheet editor to edit the
> residues of the protein.But strange thing is that in the spread sheet
> editor (editor table) I got the lists of atoms of FEW residues but NOT
> ALL. I hope this problem is with the large protein system with aqueous
> solution. As I removed most of the water molecules from the protein, it is
> being possible to edit all the aminoacid residues with all the atoms
> in the editor sheet. But I want to edit the protein in presence of all the
> water molecules in the protein system.
>
> I mailed this problem in my previous mail and got one reply to do the same
> job in LEaP command line. But I am not being able to give the appropriate
> command in the LEaP command line for the said problem. So can anybody
> please suggest how exactly I have to do this and what commands I have to
> follow in the LEaP command line to solve this problem.
>
> Thanks for your suggestions in advance.
>
> regards
> B. R. Meher --
>
>
>
>
>
> On Wed, 18 Oct 2006, Biswa Ranjan Meher wrote:
>
> > Dear Dr Scott,
> >
> > Thank you for your suggestion. But one thing I am getting problem is that my
> > protein is a large one and in an aqueous solution. While editng the protein
> > along with water I am not getting all the residues in spreadsheet editor, but
> > when I removed most of the water molecules from the protein system, it is
> > being possible to edit all the aminoacid residues with all the atoms in the
> > editor sheet.
> >
> > As you have suggested in your previous mail, "anything that can be done in
> > the editor can be done with the LEaP command line (as far as I know)". But
> > can you please suggest me how exactly I have to do this in the LEaP command
> > line.
> >
> > with regards
> >
> > B. R. Meher
> >
> >
> >
> >
> >
> >
> > On Mon, 9 Oct 2006, Scott Brozell wrote:
> >
> >> Hi,
> >>
> >> On Mon, 9 Oct 2006, Biswa Ranjan Meher wrote:
> >>
> >>>
> >>> Dear Amber users
> >>> I am having trouble with Leap. The problem is that I want to edit one
> >>> protein in xleap. I loaded one pdb file in xleap and by edit selected
> >>> atoms from the menu bar selected all the atoms of the protein. But strange
> >>> thing is that in the spread sheet editor (editor table) I got the
> >>> lists of atoms of FEW residues but NOT ALL. So my querry here is that, is
> >>> there any
> >>> tricks, which I am missing here to visualize all the atoms of all the
> >>> residues of the protein concern in the spread sheet editor?
> >>>
> >>> I am running xleap on a Linux (redhat 8.0) system.
> >>>
> >>> Has anyone else run into this problem and knows how to correct it?
> >>
> >> No. For example, I loaded 228 residue 1E1J, edited that unit,
> >> and can scroll down to what seems to be the last residue.
> >> I note that it takes a couple of seconds for the table contents to
> >> catch up to rapid scrolling and that the end of the scroll extends
> >> past the end of the contents of the table.
> >> But I do not see any obvious failure.
> >> You'll need to provide a detailed example to reproduce any problems
> >> that you have.
> >>
> >>> From a different perspective, why would one want to edit a big protein
> >> this way ? Anything that can be done in the editor can be done with
> >> the LEaP command line (as far as I know).
> >>
> >> HEADER PRION PROTEIN 08-MAY-00 1E1J
> >>
> >> Scott
> >>
> >>
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> >
> >
>
> 

-- 
  Ilyas Yildirim
  ---------------------------------------------------------------
  - Department of Chemisty       -				-
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  - http://www.pas.rochester.edu/~yildirim/			-
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