Dear AMBER users
I used ptraj (AMBER v.9) to determine contacts of desired atoms during
production MD. All the frames were successfully read. Out files were made
but did not contain any results. I tried for different atoms and other
trajectories also, but always got the following error:
*** glibc detected *** free(): invalid pointer: 0x0812bb38 ***
Aborted
Following is my ptraj script:
trajin wt.mdcrd
contacts first byresidue out 900ps-contact time 1.0 distance 8 :3.CA
Following is a part of ptraj output file:
ACTIONS
1> CONTACTS: Calculating current contacts and comparing results to
first frame
Dumping results to 900ps-contact.native,
using a time interval of 1.000000
and a cutoff of 8.000000 A
Results are output on a per-residue basis
Atom selection follows :3.CA
Processing AMBER trajectory file ../../wtATPase-900ps.mdcrd
Set 1 .................................................
Set 50 .................................................
Set 100 .................................................
Set 150 .................................................
Set 200 .................................................
Set 250 .................................................
Set 300 .................................................
Set 350 .................................................
Set 400 .................................................
Set 450 .................................................
Set 500 .................................................
Set 550 .................................................
Set 600 .................................................
Set 650 .................................................
Set 700 .................................................
Set 750 .................................................
Set 800 .................................................
Set 850 .................................................
Set 900
PTRAJ: Successfully read in 900 sets and processed 900 sets.
Dumping accumulated results (if any)
A part of contacts.native file:
#time residue 2
1.00 00
2.00 00
3.00 00
4.00 00
5.00 00
6.00 00
7.00 00
8.00 00
9.00 00
10.00 00
I found a similar error with rmsd analysis in AMBER archive but could not
get the solution to the problem.
Can anyone please tell me that what does that error indicate and what may
be problem?
Thanks in advance
Ruchi
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Received on Wed Apr 25 2007 - 06:07:40 PDT
