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
| Department of Molecular Biology TPC15 |
| The Scripps Research Institute |
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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
