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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