AMBER Archive (2005)

Subject: AMBER: ptraj

From: xueping (xueping22_at_yahoo.com)
Date: Fri Mar 11 2005 - 22:56:29 CST

Dear Amber user,

I use ptraj to calculate RMSd. This is my .ptraj file.
trajin ../PfCo.md1.mdcrd.gz
trajin ../PfCo.md2.mdcrd.gz
trajin ../PfCo.md3.mdcrd.gz
trajin ../PfCo.md4.mdcrd.gz
trajin ../PfCo.md5.mdcrd.gz
trajout PfCo_whole_md_no_wat.mdcrd
rms first out PfCo_whole_md_no_wat.rmsfit @CA time 0.1
center: 1-295
image familiar
strip:WAT

But when i run ptraj, it gives me this:
PTRAJ: Processing input file...
       Input is from standard input
 
PTRAJ: trajin ../PfCo.md1.mdcrd.gz
Checking coordinates: ../PfCo.md1.mdcrd.gz
 
PTRAJ: trajin ../PfCo.md2.mdcrd.gz
Checking coordinates: ../PfCo.md2.mdcrd.gz
 
PTRAJ: trajin ../PfCo.md3.mdcrd.gz
Checking coordinates: ../PfCo.md3.mdcrd.gz
 
PTRAJ: trajin ../PfCo.md4.mdcrd.gz
Checking coordinates: ../PfCo.md4.mdcrd.gz
 
PTRAJ: trajin ../PfCo.md5.mdcrd.gz
Checking coordinates: ../PfCo.md5.mdcrd.gz
 
PTRAJ: trajout PfCo_whole_md_no_wat.mdcrd
 
PTRAJ: rms first out PfCo_whole_md_no_wat.rmsfit @CA
time 0.1
Mask [@CA] represents 295 atoms
 
PTRAJ: center: 1-295
WARNING: Error in mask string, no "@" or ":" present
(1-295)
 
PTRAJ: image familiar
Mask [*] represents 28172 atoms

PTRAJ: strip:WAT
Segmentation fault (core dumped)

Any suggestion?

Thank you very much.

Regards
xueping

                
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