Indeed the center of mass calculation (of the whole masked atoms) is really
easy to implement just adding a few lines there. Nevertheless, my interest
is slightly different.I'm trying to figure out how to modify the code so
the mask could include different residues, and then, the center of mass
should be per residue (e.g. my system is solvated in a mixture of water and
ethanol and would like to obtain a density grid for each ethanol residue's
center of mass).
I guess state->residues should here play some role but I'm not sure how to
proceed as I don't know the structure of the program or variables, or if
there are some functions already implemented to make this task easier? Is
there some other function which implements a similar routine?
Thanks again Dan!
---------- Forwarded message ----------
From: Daniel Roe <daniel.r.roe.gmail.com>
Date: 2012/11/26
Subject: Re: [AMBER] ptraj grid by center of mass
To: AMBER Mailing List <amber.ambermd.org>
Hi,
Currently 'grid' doesn't do what you would like, but it shouldn't be too
difficult to modify the code. Take a look at actions.c around line 9207.
You can change the loop there so you calculate the center coords of the
atoms in the mask into temporary vars (e.g. tempX, tempY, and tempZ), then
grid the temp. coords using the same procedure from line 9212 onward.
Good luck!
-Dan
On Mon, Nov 26, 2012 at 6:55 AM, Daniel Álvarez García <
algarcia.daniel.gmail.com> wrote:
> Dear AMBER developers,
>
> ptraj's grid command is very useful to build density grids for the given
> atoms in the mask.
> However I am interested in building the density grid for the center of
mass
> of the atom group
> given in the mask. Is it posible with the current Ambertools12 version of
> ptraj?
> Otherwise, would it be easy to modify the source code to allow such
> implementation of grid?? Any advice or
> tips on how to modify the code or use this feature will be highly
> appreciated!!
>
> Thanks in advance,
>
> Daniel
>
> --
> Daniel Álvarez
> algarcia.daniel.gmail.com
> PhD Student
> Computational Biology and Drug Discovery Group, UB
> http://www.ub.edu/cbdd/
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-9119 (Fax)
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--
Daniel Álvarez
algarcia.daniel.gmail.com
PhD Student
Computational Biology and Drug Discovery Group, UB
http://www.ub.edu/cbdd/
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Received on Mon Nov 26 2012 - 10:30:02 PST
