AMBER Archive (2007)

Subject: AMBER: I need some help in PTRAJ

From: Vijay Manickam Achari (vjrajamany_at_yahoo.com)
Date: Mon Dec 03 2007 - 00:49:29 CST


I am simulating bilayer sistem in water.
 I break my longer simulation period into smaller
 fractions where by each contain 1000 frames.
 At first I reimage the system so that all the waters
 are in the box using below code:

 trajin ../betaM_lyo_md02_0900.mdcrd.gz
 trajout betaM_lyo_md02_0900.mdcrd mdcrd
 center :1-256
 image center familiar

 the output of this run is as below.

 DDM DDM DDM DDM DDM DDM DDM DDM DDM DDM
 ...
 DDM DDM DDM DDM DDM DDM WAT WAT WAT WAT
 WAT WAT WAT WAT WAT WAT WAT WAT WAT WAT
 ...
 WAT WAT WAT WAT WAT WAT WAT WAT
 Scanning Box
 Successfully completed readParm.
 PTRAJ: Processing input file...
 Input is from standard input
 PTRAJ: trajin ../betaM_lyo_md02_0900.mdcrd.gz
 PTRAJ: trajout betaM_lyo_md02_0900.mdcrd mdcrd
 PTRAJ: center :1-256
 Mask [:1-256] represents 20736 atoms
 PTRAJ: image center familiar
 Mask [*] represents 23832 atoms
 PTRAJ: Successfully read the input file.
 Coordinate processing will occur on 999 frames.
 Summary of I/O and actions follows:
 INPUT COORDINATE FILES
 File (../betaM_lyo_md02_0900.mdcrd.gz) is an AMBER
 trajectory (with box info) with 999 sets
 OUTPUT COORDINATE FILE
 File (betaM_lyo_md02_0900.mdcrd) is an AMBER
 trajectory (with box info)
 ACTIONS
 1> CENTER to box center via center of geometry, atom
 selection follows :1-256
 7> IMAGE familiar by molecule to box center using
 the center of mass, atom selection * (All atoms are
 selected)
 IMAGE familiar, center is at box center

 Processing AMBER trajectory file
 ../betaM_lyo_md02_0900.mdcrd.gz
 Set 1
 .................................................
 Set 50
 .................................................
 Set 100
 .................................................
 Set 150
 .................................................
 Set 200
 .................................................
 Set 250
 .................................................
 Set 300 .....................

PTRAJ: Successfully read in 321 sets and processed
 321 sets.
 Dumping accumulated results (if any)
***********************************************************

 Actually it supposed read 1000 frames, but it
 reads only 321 frames.

 When I check the mdcrd file for any characters such
 as (*) .. I can't find any thing like this.

 In one nanosecond simulation I have 10 files with
 each 1000 frames.
 But some files are not shwoing any message like this
 in output file, but some are showing message like
 this.

 I need help to overcome this problem.

 I also done simulation again and again few times.
 But the results are still the same.

 Any expert can help me?
 I really appreciate your help.

 Thank you.

 Vijay

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