Hello,
I'm trying to calculate free energies of binding (for complex between
DNA and small molecule) with MM_PBSA method. I run the following
command: "mm_pbsa.pl mm_pbsa_Binding.in > mm_pbsa_Binding.log" and
after few minutes I got the message: "No data for 0+1 MM BOND 480". In
my new log file there is no final part for statistics. I also tried to
run mm_pbsa_statistics.pl (because it produced three intermediate
files: snapshot_DNA_TD22_2_com.all.out,
snapshot_DNA_TD22_2_rec.all.out and snapshot_DNA_TD22_2_lig.all.out)
but after running it I became:
=>> Reading input
=>> Reordering files
Final order:
1. snapshot_DNA_TD22_2_com.all.out: -
2. snapshot_DNA_TD22_2_rec.all.out: -
3. snapshot_DNA_TD22_2_lig.all.out: -
=>> Reading files
=>> Values of parameters
TEMP = 300
R = 8.314
=>> Treat special parameters
=>> Calc missing parameters
=>> Calc average and stddev
=>> Print output (decomp) to snapshot_DNA_TD22_2_statistics.out
snapshot_DNA_TD22_2_statistics.out not opened
...and, of course, no statistics output file.
Btw, we installed Amber 10 just few days ago and patched the latest
version of bug fixes.
I would be very grateful if anyone could help me to fix this problem...
Best regards,
Marina
--
Marina Grabar, B.Sc.
Institute Rudjer Boskovic
Bijenicka 54
HR-10000, Zagreb
CROATIA
tel +385-1-4561025
fax +385-1-4680245
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Feb 11 2010 - 07:00:03 PST
