AMBER Archive (2005)

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

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Wed Mar 23 2005 - 12:13:56 CST

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

/\
\/
|\oss Walker

| Department of Molecular Biology TPC15 |
| The Scripps Research Institute |
| Tel:- +1 858 784 8889 | EMail:- ross_at_rosswalker.co.uk |
| http://www.rosswalker.co.uk/ | PGP Key available on request |

Note: Electronic Mail is not secure, has no guarantee of delivery, may not
be read every day, and should not be used for urgent or sensitive issues.

 

  _____

From: owner-amber_at_scripps.edu [mailto:owner-amber_at_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 .

 

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu