AMBER Archive (2009)

Subject: [AMBER] RE: ERROR in ptrajInitializeState(): Attempting ....

From: Siavoush Dastmalchi (Dastmalchi.s_at_tbzmed.ac.ir)
Date: Sat May 30 2009 - 12:11:55 CDT


Hi there,
 
Sorry for my previous question. The problem was just a bad file name. Looks like that "egf_egfr_solvated.prmtop" was not a good choice.
 
Cheers, siavoush

________________________________

From: amber-bounces_at_ambermd.org on behalf of Siavoush Dastmalchi
Sent: Sat 2009/05/30 07:36 .
To: AMBER Mailing List
Subject: ERROR in ptrajInitializeState(): Attempting ....

Dear List,
 
I am trying to use ptraj and my script has the name of mdcrd files and the action command. I am also providing the prmtop file, but I get the following error massages:
 
Could not open file (egf_egfr_solvated.prmtop) with mode (r)
ERROR in ptrajInitializeState(): Attempting to open parameter/topology file egf_egfr_solvated.prmtop

My prmtop file looks okay to me, however I need to mention that it is a solvated system and the size of the prmtop file is ~14 Mb. Is there any size limitation for ptraj?
 
Cheers, Siavoush

________________________________

From: amber-bounces_at_ambermd.org on behalf of Bill Ross
Sent: Thu 2009/05/28 04:22 .
To: amber_at_ambermd.org
Subject: Re: [AMBER] problem with MM-PBSA

> I visualized the trajectories, I realized that atoms are moving too far
> making bad bond lengths and angles. Gradually, some of the residues
> (atom by atom) move to new locations still keeping their links (very
> long bonds).

This happens when residues cross the edge of the periodic box and
are translated to the other side. If you are running periodic, search
the archive for 'ptraj image'.

Bill

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