AMBER Archive (2006)

Subject: AMBER: Performing Interactive Essential Dynamics in Ptraj

From: hbluo (hbluo_at_hkbu.edu.hk)
Date: Thu Nov 30 2006 - 18:58:11 CST

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/),

---------------------------------------------------------------------------------------
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
------------------------------------------------------------------------------------------

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_at_hkbu.edu.hk & hbluo2005_at_yahoo.com.cn
Department of Chemistry, Hong Kong Baptist University,
Kowloon Tong, Hong Kong
Voice:(852)3411-5815
Fax:(852)3411-7348

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu