AMBER Archive (2004)

Subject: Re: AMBER: Moil-view, prmtop, inpcrd question

From: opitz_at_che.udel.edu
Date: Mon Aug 16 2004 - 14:18:50 CDT

('binary' encoding is not supported, stored as-is) I downloaded the new version from the website (http://morita.chem.sunysb.edu/~carlos/viewpage/download.html), but I am not familiar with the file extension of this file. The file I downloaded was moil-view.10.2.r10k , how do I go about installing it? (or is it the same of what Viktor had said earlier?)
==============Original message text===============
On Mon, 16 Aug 2004 14:45:08 EDT Viktor Hornak wrote:

It's as Dave Case suspected: this version of Moil-view didn't recognize
the correct format for number of atoms (notice that Moil-view thinks
your molecule has 22 atoms, see below, while it really has 228 atoms;
this is the issue of I5 vs. 'new' I6 format on reading). Get the new
version of Moil-view where this problem is fixed...

-Viktor

opitz_at_che.udel.edu wrote:
> Here is the text moil-view writes to the shell window:
>
> MOIL_View version 10
> by Carlos Simmerling
> carlos.simmerling_at_sunysb.edu
> Portions were written while in the groups of:
> Ron Elber at the University of Illinois at Chicago and
> Peter Kollman at the University of California, San Francisco
>
> Color table entries, R,G,B
> 0 0 0
> Color table entries, R,G,B
> 0 125 125 125
> 1 255 0 0
> 2 255 125 0
> 3 255 255 0
> 4 125 255 0
> 5 0 255 0
> 6 0 255 125
> 7 0 255 255
> 8 0 125 255
> 9 0 0 255
> 10 125 0 255
> 11 255 0 255
> 12 255 0 125
> This system's graphics version: GL4DSLD-6.5
> Using double buffered RGB mode
> Using 5 red bitplanes
> Using 5 green bitplanes
> Using 5 blue bitplanes
> screen size is x: 1280 y: 1024
> Blending will be used
> Reading MOIL-View session file version 10.00
> read all filenames
> Reading AMBER format coordinates
>
> 22 atoms present
.............^^
incorrect number of atoms here.

> read coordinates
> read velocities
> read box coordinates 2.325412 1.984545 -9.193504
> xmax, xmin 7.548902 3.049519
> ymax, ymin 2.888557 -5.979939
> zmax, zmin -5.294160 -8.554189
> | New format PARM file being parsed.
> | Version = 1.000 Date = 08/13/04 Time = 15:43:04
> 1 total line objects
> nothing picked!
>
> One thing I can see looking at this is that I do not have periodic
> boundaries, but it seems to be looking for them. I am pretty sure that
> moil-view is set not to look for boundaries with the settings I have.
> I have not reinstalled it yet, as I wanted to see what the analysis of
> this text would give first.

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