Dear Amber users,
Who has performed essential dynamics in ptraj?
According to the instruction to prepare input for Interactive Essential Dynamics using ptraj (
http://mccammon.ucsd.edu/ied/),
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trajin <trajectory file>
rms first *
matrix covar name mcovar
analyze matrix mcovar out evec.pev vecs 25
go
trajin <trajectory file>
rms first *
projection modes evec.pev out proj.ppj beg 1 end 25
go
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there are some errors and no output was observed in my exercise (AMBER 9.0).
+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
PTRAJ: trajin 1ere-est_md1.mdcrd
Checking coordinates: 1ere-est_md1.mdcrd
PTRAJ: rms first *
Mask [*] represents 33969 atoms
PTRAJ: projection modes evec.pev out proj.ppj beg 1 end 25
WARNING in dispatchToken: Token string "projection" not found in tokenlist
WARNING in dispatchToken: Token string "modes" not found in tokenlist
WARNING in dispatchToken: Token string "evec.pev" not found in tokenlist
WARNING in dispatchToken: Token string "out" not found in tokenlist
WARNING in dispatchToken: Token string "proj.ppj" not found in tokenlist
WARNING in dispatchToken: Token string "beg" not found in tokenlist
WARNING in dispatchToken: Token string "1" not found in tokenlist
WARNING in dispatchToken: Token string "end" not found in tokenlist
WARNING in dispatchToken: Token string "25" not found in tokenlist
FYI: No output trajectory specified (trajout), none will be saved.
PTRAJ: Successfully read the input file.
Coordinate processing will occur on 20 frames.
Summary of I/O and actions follows:
INPUT COORDINATE FILES
File (1ere-est_md1.mdcrd) is an AMBER trajectory (with box info) with 20 sets
OUTPUT COORDINATE FILE
NULL entry
ACTIONS
1> RMS to first frame using no mass weighting
Atom selection follows * (All atoms are selected)
Processing AMBER trajectory file 1ere-est_md1.mdcrd
Set 1 ....................
PTRAJ: Successfully read in 20 sets and processed 20 sets.
Dumping accumulated results (if any)
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
I would appreciate for any suggestion or help.
Best wishes!
---------
Hai-Bin Luo
hbluo.hkbu.edu.hk & hbluo2005.yahoo.com.cn
Department of Chemistry, Hong Kong Baptist University,
Kowloon Tong, Hong Kong
Voice:(852)3411-5815
Fax:(852)3411-7348
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Received on Sun Dec 03 2006 - 06:07:24 PST
