Hello again,
I forgot to add this: I used pymdpbsa in AmberTools 12.
Thanks,
Genzo
> From: gmastanaka.msn.com
> To: amber.ambermd.org
> Date: Mon, 14 May 2012 12:57:46 -0400
> Subject: [AMBER] Periodicity errors in pymdsapb
>
>
> Hello,
> A periodicity error occurred during a calculation for the free energy of binding in pymdpbsa using a molecular dynamics file from mdnab:
> % pymdpbsa --proj=test,--traj=traj.binpos,--cprm=com.prm,--lprm=lig.prm,--rprm=rec.prm,lig=flmfoh1,--start=1,--stop=1000,--step=200,--solv=1,--clean & % Found an invalid periodicity in the prmtop file: 5failure in molsurfTraceback (most recent call last): File "/Users/genzotanaka/Downloads/amber12/bin/pymdpbsa", line 770, in <module> opt.start, opt.stop, opt.step, gb, sa) File "/Users/genzotanaka/Downloads/amber12/bin/pymdpbsa", line 95, in nrgtable_gb etot, ebat, evdw, ecoul, egb, sasa = ffgbsa(prmtop, pdbfile, gb, sa) File "/Users/genzotanaka/Downloads/amber12/bin/pymdpbsa", line 271, in ffgbsa etot = etot + sasaUnboundLocalError: local variable 'etot' referenced before assignment
>
>
> A protein and a ligand were created by x-leap, and the charges of ligand was assigned by a sqm calculation. The ligand was checked by the unit check until no error occurred by generating the necessary force field parameters. The ligand contains a florine atom, whose force field data was provided by our myparam.dat. No solvent box was generated since we want to do an implicit solvent case.
> By the way, when I used our file names for traj, cprm, lprm, etc, I got errors (files were not found). However, the temporary directories were created (I am not sure I can ignore this error message, since our computation hasn't been successful).
>
> I would appreciate your help.
> Thanks,
> Genzo
>
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>
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Received on Mon May 14 2012 - 10:30:03 PDT
