AMBER Archive (2004)

Subject: Re: AMBER: MAXRMSPT error in MOIL-view

From: Carlos Simmerling (carlos_at_ilion.bio.sunysb.edu)
Date: Thu Jul 01 2004 - 17:26:53 CDT

MAXRMSPT is in RMSMAT.BLOCK.

be careful of making it too big, because it
saves coordinates for all of these atoms
for each frame in order to construct the RMSD matrix.
991 should not be a problem, though.
carlos

----- Original Message -----
From: "Robyn Ayscue" <kajsicat_at_yahoo.com>
To: <amber_at_scripps.edu>
Sent: Thursday, July 01, 2004 6:19 PM
Subject: AMBER: MAXRMSPT error in MOIL-view

> All,
>
> I'm having a problem trying to run a cluster
> trajectory with MOIL-view (I've tried this on versions
> 10.2 and 9.1). The molecule I'm working with is a
> modified DNA thymidine 15-mer (no solvent, no ions),
> and I'm using an SGI machine running IRIX 6.5.24.
>
> First, I load a .pdb file using distance bonds, and
> then I slect "cluster trajectory" from the right-click
> menu. It asks me if I want to load data from a file
> and I click "no," so it give me the pick command line.
> I type "pick chem prtc * done," because I want to
> select all the atoms in the system. As soon as I enter
> the pick command and click "done," it tells me the
> number of selected particles ("# selected = 991, Click
> to continue"). But when I click on that dialogue box
> it then says "Exceeded MAXRMSPT" and doesn't go any
> further. I tried to enter a different pick ("pick #mon
> 1 30 done," because there are 30 bases in my oligo)
> and I still get the same error. Then I tried to raise
> the limit of the MAXRMSPT and MAXRMSFT parameters in
> the LENGTH.BLOCK file, as per the instructions in the
> manual, but I didn't see those parameters listed
> there. Has anyone else been afflicted with this? Any
> help would be greatly appreciated.
>
> Yours,
> Robyn Ayscue
>
>
>
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