Which function of mm_pbsa.pl are you using, for example, gb, pb?
On Thu, Feb 11, 2010 at 9:51 AM, Marina Grabar <Marina.Grabar.irb.hr> wrote:
> 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
>
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>
--
T. Dwight McGee Jr.
Quantum Theory Project
University of Florida
dwight.mcgee.gmail.com
"Problems cannot be solved at the same level of awareness that created
them."
Albert Einstein
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Received on Thu Feb 11 2010 - 07:30:02 PST
