RE: AMBER: Could not open file (trajin) with mode (r)

From: Ross Walker <ross.rosswalker.co.uk>
Date: Wed, 23 Mar 2005 10:13:56 -0800

You aren't running ptraj correctly. You need to specify the prmtop file.
 
In the DNA tutorial under section 3.3.2 you should be creating a txt file
with the contents:
 
trajin polyAT_vac_md1_12Acut.mdcrd
rms first mass out polyAT_vac_md1_12Acut.rms time 0.1
 
And then save this file as polyAT_vac_md1_12cut.calc_rms
 
You then run ptraj with the command:
 
ptraj polyAT_vac.prmtop < polyAT_vac_md1_12Acut.calc_rms
 
If you do this then it should work correctly.
 
All the best
Ross

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|\oss Walker

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  _____

From: owner-amber.scripps.edu [mailto:owner-amber.scripps.edu] On Behalf Of
Maciej
Sent: 23 March 2005 05:52
To: amber
Subject: AMBER: Could not open file (trajin) with mode (r)



During one of tutorials when i could do that

ptraj trajin polyAT_vac_md1_12Acut.mdcrd rms first mass out
poluAT_vac_md1_12Acut.rms time 0.1 i have msg

Amber8 Module: ptraj

 

 

Could not open file (trajin) with mode (r)

 

ERROR in ptrajInitializeState(): Attempting to open parameter/topology file
traj in ..

I thought that was read mode not set to taht file but it wasnt that .

What i have wrong ?? Please help me .

 



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Received on Wed Mar 23 2005 - 18:53:01 PST
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