From: Zhiguo Liu <>
Date: Sat, 9 Jul 2005 16:39:43 +0800

Dear glc0358,
   Most of time this is because you have used an improper topology pdb file to parse your trajectory, e.g., the trajectory has water included, whereas your topology pdb file includes only protein, or vice versa. In a word, your topology file should be corresponding to your trajectory file.

                                                             Zhiguo Liu

Zhiguo Liu
Ph.D candidate
Drug Discovery and Design Center
Shanghai Institute of Materia Medica
Chinese Academy of Science
Shanghai, China

----- 2005-07-09, 15:03:23, glc0358 wrote -----

>Hi all.
>I'm using amber7 for md simulation. I created a GDP molecule and simulated it in explicit water. The minimization step is OK, however, when I ran md with SANDER and visualized the trajectory with vmd, I found that the system became into a mass, the bonds were stretched to terrible long.
>To diagnose the reason, I tried the example of polyA-T tutorial, the same phenomena appeared. At the same time, the data in mdout file seemed stable, but was different with tutorial.
>I checked the FAQ,I'm not sure whether it was the so-called blowup. Could anyone tell me why?
>Linchen Gong
>department of physics
>Tsinghua University
>The AMBER Mail Reflector
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Received on Sat Jul 09 2005 - 09:53:01 PDT
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