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#19857 01/17/09 05:16 PM
Joined: Jul 2004
Posts: 165
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Dear all,

I have analyzr hydrogen bond with charmm version c35 and following is output Analysing hydrogen bond patterns for:
#donors #acceptors
1st sel: 73 32
2nd sel: 224 448


READING TRAJECTORY FROM UNIT 30
NUMBER OF COORDINATE SETS IN FILE: 48134
NUMBER OF PREVIOUS DYNAMICS STEPS: 500
FREQUENCY FOR SAVING COORDINATES: 500
NUMBER OF STEPS FOR CREATION RUN: 24067000

TITLE> * GENERATE POPG LIPID
TITLE> * DATE: 1/13/ 9 22:53:52 CREATED BY USER: jutarat
TITLE> *
***** WARNING ***** BEGIN= 0 Was not specified. It has been set to: 5000

4813 CORD RECORDS READ FROM 1 UNITS STARTING WITH UNIT 30
RUNNING FROM STEP 5000 TO 24065000 SKIPPING 5000 STEPS BETWEEN RECORDS
Time step was 0.000000 AKMA time units.


hydrogen bonds. Total time= 0.0ps. Resolution= 0.000ps.
Cutoff distance= 2.40 time= 0.0 occupancy= 0.00
ATOM <occupancy> <lifetime> (ps)
-----------------------------------------------------
OVERALL
Average number (over ISEL!)= 0.000
<lifetime>= 0.00ps
Total number/frame= 0.0
however, if I did the same with c33, it went well.

Do you have any suggestion? does it installation problem?

thank you

beginner #19858 01/17/09 07:37 PM
Joined: Sep 2003
Posts: 4,833
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A bit strange. Timestep 0.0000? The hydrogen bond analysis code is the same in c33b1 and c35b1. Do the testcases (in particular hba1 and hba2) run with your c35 installation, and do they give similar results as with c33?


Lennart Nilsson
Karolinska Institutet
Stockholm, Sweden

Moderated by  lennart, rmv 

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