AMBER Archive (2008)

Subject: AMBER: How to convert a CHARMM trajectory to AMBER format?

From: Jeffrey (jeffry20072008_at_yahoo.cn)
Date: Tue Aug 19 2008 - 06:30:35 CDT

Dear all,

     I am new to amber. So could someone please tell me how to convert a md trajectory generated in CHARMM to AMBER format? I write the following script.amber, but it doesn't work... 

----
ptraj prot0-10090.psf << EOF
trajin orient0-10090prot.dcd 1000 10090000 1000
trajout amber.traj
EOF
----

When run the script by "ptraj script.amber", the following message was displayed:
---
  \-/  
  -/-   PTRAJ: a utility for processing trajectory files
  /-\  
  \-/   Version: "AMBER 9.0 integrated" (April 2006)
  -/-   Executable is: "ptraj"
  /-\  
  \-/   Error scanning a value: parm->NTOTAT
Error scanning a value: parm->NTYPES
Error scanning a value: parm->NBONH
Error scanning a value: parm->NTHETH
Error scanning a value: parm->JHPARM
Error scanning a value: parm->JPARM
Error scanning a value: parm->NEXT
Error scanning a value: parm->NTOTRS
Error scanning a value: parm->MBONA
Error scanning a value: parm->MTHETS
Error scanning a value: parm->MPHIA
Error scanning a value: parm->MUMBND
Error scanning a value: parm->MUMANG
Error scanning a value: parm->IFPERT
Error scanning a value: parm->NBPER
Error scanning a value: parm->NGPER
Error scanning a value: parm->NDPER
Error scanning a value: parm->MBPER
Error scanning a value: parm->MGPER
Error scanning a value: parm->MDPER
Error scanning a value: parm->IFBOX
Error scanning a value: parm->NMXRS

ERROR in NAME_COPY: ... EOF encounters on scanning igraph
----

Any suggestion is greatly appreciated.
Thanks very much for the time.

Have a nice day.

-------
Jeffrey

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