AMBER Archive (2004)

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

From: opitz_at_che.udel.edu
Date: Mon Aug 16 2004 - 13:17:35 CDT

('binary' encoding is not supported, stored as-is) 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
 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.

Armin

==============Original message text===============
On Sat, 14 Aug 2004 8:13:23 EDT Carlos Simmerling wrote:

can you send the text that moil-view writes to the shell window?
send the error message line(s) and at least a dozen of the lines it
writes before that.
carlos

===================================================================
Carlos L. Simmerling, Ph.D.
Assistant Professor Phone: (631) 632-1336
Center for Structural Biology Fax: (631) 632-1555
Stony Brook University Web: http://comp.chem.sunysb.edu/carlosStony Brook, NY 11794-5115 E-mail: carlos.simmerling_at_stonybrook.edu
===================================================================

opitz_at_che.udel.edu wrote:

>Dear Amber Community,
>
>I am trying to load a molecule in moil-view10 using a prmtop and inpcrd
>file generated by xleap.
>At first I load the coordinate file. When it prompts to use connectivity
>files I choose yes and load my prmtop file. At this point the warning:
>CRD/CON mistmatch in #atom
>appears.
>I checked the inpcrd and prmtop files and they seemed fine. I don't know
>if this is a moil-view problem, and I don't know how I would fix it (if
>the problem lies here, I would greatly appreciate very detailed help).
>I have attached the two files in question.

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