AMBER Archive (2005)

Subject: Re: AMBER: Can we load prmtop and inpcrd files into xleap?

From: Ilyas Yildirim (yildirim_at_pas.rochester.edu)
Date: Wed May 18 2005 - 23:47:49 CDT

I also use a .lib file for my case. The only thing is the following: I
will be doing free energy simulation for 2 cases: from state 0 to state 1;
and from state 1 to state 0. And I want to start from the same atomic
coordinates for each case (except the atoms which will be perturbed). I
have ions/water/residue in my system. I want in both case the same numbers
of water molecules (and exactly in the same coordinates). When I create
both residues and save them in a .lib file, I have to solvate them
seperately, and they wont give me the same number of water molecules and
neither the same coordinates.

In any case, I was just thinking if its possible to load the .prmtop and
.inpcrd files at the same time and get all the info in Xleap. Thanks for
your suggestion though.

On Wed, 18 May 2005, Kara Di Giorgio wrote:

> I guess I never thought of that. Good question. I created .lib files
> for some of my portions that I had to change types/add charges so I can
> just loadoff X.lib and it's now there so when I load my pdb, it knows
> that portion already. Maybe this can help you.
>
> Kara
>
> On May 18, 2005, at 9:00 PM, Ilyas Yildirim wrote:
>
> > Thats true; xleap is to create the prmtop/inpcrd files. But sometimes,
> > I
> > wanna do some changes on the structure (like changeing the
> > type/charge).
> > In that case, I have to follow every step again; create the .pdb file,
> > load it into xleap, play with the types/charges/etc... If it is
> > possible
> > to load everything from .prmtop and .inpcrd file into xleap, I can
> > easily
> > change whatever I want to.
> >
> > On Wed, 18 May 2005, Kara Di Giorgio wrote:
> >
> >> I thought the main use for xLEaP was to CREATE prmtop and inpcrd
> >> files
> >> for other parts of amber (ie sander). Maybe I'm mistaken, though.
> >>
> >> Kara Di Giorgio
> >>
> >> On May 18, 2005, at 7:16 PM, Ilyas Yildirim wrote:
> >>
> >>> Hi all,
> >>>
> >>> If we have a .prmtop and .inpcrd file, we can create a .pdb file
> >>> using
> >>> ambpdb. And after getting the .pdb file, we can load it into xleap
> >>> with
> >>> 'loadpdb' command. I was wondering if we can load any .prmtop and
> >>> .inpcrd
> >>> files into xleap directly? The .prmtop file has all the atom
> >>> type/charge/perturbation/etc... informations in it, and that will be
> >>> pretty fast to load all these info into xleap. Thanks in advance.
> >>>
> >>> Best,
> >>>
> >>> --
> >>> Ilyas Yildirim
> >>> ---------------------------------------------------------------
> >>> - Department of Chemisty - -
> >>> - University of Rochester - -
> >>> - Hutchison Hall, # B10 - -
> >>> - Rochester, NY 14627-0216 - Ph.:(585) 275 67 66 (Office) -
> >>> - http://www.pas.rochester.edu/~yildirim/ -
> >>> ---------------------------------------------------------------
> >>>
> >>> ---------------------------------------------------------------------
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> >>> The AMBER Mail Reflector
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> >
> > --
> > Ilyas Yildirim
> > ---------------------------------------------------------------
> > - Department of Chemisty - -
> > - University of Rochester - -
> > - Hutchison Hall, # B10 - -
> > - Rochester, NY 14627-0216 - Ph.:(585) 275 67 66 (Office) -
> > - http://www.pas.rochester.edu/~yildirim/ -
> > ---------------------------------------------------------------
> >
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-- 
  Ilyas Yildirim
  ---------------------------------------------------------------
  - Department of Chemisty       -				-
  - University of Rochester      -				-
  - Hutchison Hall, # B10        -				-
  - Rochester, NY 14627-0216     - Ph.:(585) 275 67 66 (Office)	-
  - http://www.pas.rochester.edu/~yildirim/			-
  ---------------------------------------------------------------

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