RE: AMBER: Unable to open MDCRD file using vmd

From: Ross Walker <ross.rosswalker.co.uk>
Date: Thu, 23 Aug 2007 13:40:27 -0700

Hi Priya,
 
If your mdcrd file is larger than 2GB it is very likely that VMD won't read
it. You can use ptraj to split it up into chunks or alternatively build a
smaller file with say only every 100th step in it.
 
Also VMD cannot deal with pathnames longer than a certain number of
characters - I don;t know the exact number, probably 128 or 256. Either way
it manifests itself as an "unable to open" message so you may want to check
the length of your path and try moving it to a shorter directory tree.
 
Good luck
Ross

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From: owner-amber.scripps.edu [mailto:owner-amber.scripps.edu] On Behalf Of
priya priya
Sent: Thursday, August 23, 2007 08:04
To: amber.scripps.edu
Subject: AMBER: Unable to open MDCRD file using vmd


Dear all,

i have run implicit solvent simulations for 30ns,and for output frequency i
have given ntwx=50, so i have a big mdcrd file, i want to see the folding
patway of my protein,but i am not able to open my mdcrd file using vmd1.8.3,
i am using amber9.
steps to open mdcrd file i followd are
1. opened prmtop file using parm7 option and then loaded mdcrd file and
selected crd option , but it says unable to load molecule, i have seen mdcrd
file,it seems to be ok,but it is not working,
may i know where the problem is.
i have tred to open 100ps mdcrd file using vmd it is working.

Regards
priya




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Received on Sun Aug 26 2007 - 06:07:31 PDT
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