AMBER Archive (2005)

Subject: AMBER: MM_PBSA stopped at some snapshot

From: Xioling Chuang (xioling_c_at_hotmail.com)
Date: Mon Nov 28 2005 - 23:57:54 CST

Dear All,

I have used mm_pbsa to extract 1000 snapshots of complex (DNA duplex),
receptor (1st strand), and ligand (2nd strand). When mm_pbsa calculated PB
upto snapshot 359, pbsa output stopped with message
---File "pbsa_com.359.out" ---
.
.
.
Iteration data
   Maximum iterations : 500
   Convergence criteria: 1.000000000000000E-003
   Iterations required : 12
   Norm of the constant vector: 7829.90318844151
   Norm of the residual vector: 4.66126368647964
   Convergence achieved : 5.953156219556570E-004

PB Bomb in epsbnd(): No neighbor found for exposed boundary grid 51
          79 32
----------------------------

1. Is this problem caused by bad geometry of complex? I have visualed the
molecule and it looked fine.
2. What should I solve the problem to complete the pbsa calculation of all
snapshots?
3. If this is a problem of a bad geometry of snapshot, how mm_pbsa.pl
ignores such snapshot and continue the next snapshots in order to complete
the calculation?

Thank you very much in advance.

Best Regards,
Xioling

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