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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Received on Tue Nov 29 2005 - 06:53:01 PST
