Hi,
On Wed, 25 Apr 2007, Ruchi Sachdeva wrote:
> 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
A classically almost useless error message.
Apparently, free is passed a pointer to non-dynamic or
otherwise inappropriate memory.
Since there are 1091 instances of 'free' in src/ptraj
and an unknown but maybe large number of uses of 'free' in glibc,
more clues will be needed to easily track this down.
If you send all the necessary input files then I can crank
up valgrind.
> 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 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
...
> 10.00 00
>
> I found a similar error with rmsd analysis in AMBER archive but could not
> get the solution to the problem.
http://archive.ambermd.org/200610/0396.html
Scott
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Sun Apr 29 2007 - 06:07:40 PDT
