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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Received on Sat Mar 12 2005 - 05:53:01 PST
