AMBER Archive (2007)

Subject: AMBER: RE: tutorial file polyAT_vac.prmtop

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Sun Aug 05 2007 - 22:09:46 CDT

Hi Stan,
 
Assuming you selected AMBER7 Parm as the file type I suspect what you might
be seeing is a bug that is inherent in VMD. Basically it can't handle
pathnames that are too long, it seems they don't dynamically allocate the
buffer to store the pathname. So if you have quite a deep path hierachy to
where you saved the prmtop file this might be the problem. Try copying it to
a shorted path like /tmp and then see if that works.
 
I have reported this very annoying bug to the VMD developers several times
but still they have not offered a fix to what should be a simple problem to
solve. :-(
 
All the best
Ross

  _____

From: Domitila Kaczmarczyk [mailto:domitilak_at_comcast.net]
Sent: Sunday, August 05, 2007 18:56
To: amber_tutorial_query_at_rosswalker.co.uk
Subject: tutorial file polyAT_vac.prmtop

Hi Dr Walker.
I am following yours instructions in tutorial B1. I am trying to open
polyAT_vac.prmtop in vmd 1.8.6 and i am getingmessage "unable to load
molecule".
 The file is copied from you tutorial without any modifications. Could you
please tell me what I am doing wrong. I tried different versions of vmd with
the same outcome.
Regards Stan.K
Kaczmarczyks_at_ncifcrf.gov

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