I have not tried this myself but I suspect that it is the extra point in
opc that is a problem if you keep explicit water in the pb calculation. You
might try stripping all of those, even for the water you keep.
On Mon, Oct 24, 2022, 7:16 AM Antonija Tomić via AMBER <amber.ambermd.org>
wrote:
> Dear Amber Users,
>
> I have the similar problem as already asked on the mailing list
> (http://archive.ambermd.org/202109/0046.html).
> Namely I try to run mmpbsa analysis with a couple of explicit water
> molecules defined as part of the complex. This worked fine when working
> with trajectories (and .prmtop) that had been generated using ff14SB +
> TIP3P but seems to no longer work when using trajectories generated with
> ff19SB + OPC.
>
>
> I use the following script (:WAT are removed from strip_mask as analysis
> is preformed on already striped trajectory - trajectory with defined
> number of water molecules and prepared by closest command):
>
> Input file
> &general
> interval=5,
> verbose=2, keep_files=0,
> startframe=1801,
> endframe=2000,
> strip_mask=:Cl*,CIO,Cs+,IB,K*,Li+,MG*,Na+,Rb+,CS,RB,NA,F,CL,
> /
> &gb
> igb=5, saltcon=0.020,
> /
> &pb
> indi=2, istrng=0.020, radiopt=0,
> /
>
> Job performed with ff19sb + opc stops with the following error:
>
> Running calculations on normal system...
>
> Beginning GB calculations with /usr/local/amber20/bin/mmpbsa_py_energy
> calculating complex contribution...
> calculating receptor contribution...
> calculating ligand contribution...
>
> Beginning PB calculations with /usr/local/amber20/bin/mmpbsa_py_energy
> calculating complex contribution...
> File "/usr/local/amber20/bin/MMPBSA.py.MPI", line 100, in <module>
> app.run_mmpbsa()
> File
> "/usr/local/amber20/lib/python3.9/site-packages/MMPBSA_mods/main.py",
> line 218, in run_mmpbsa
> self.calc_list.run(rank, self.stdout)
> File
> "/usr/local/amber20/lib/python3.9/site-packages/MMPBSA_mods/calculation.py",
>
> line 82, in run
> calc.run(rank, stdout=stdout, stderr=stderr)
> File
> "/usr/local/amber20/lib/python3.9/site-packages/MMPBSA_mods/calculation.py",
>
> line 428, in run
> error_list = [s.strip() for s in out.split('\n')
> TypeError: a bytes-like object is required, not 'str'
> Error occured on rank 0.
> Exiting. All files have been retained.
>
> I must emphasize that I have no problem visualizing the trajectories of
> the complex, receptor and ligand in VMD.
> I have radiopt=0 in my PB namelist as suggested
> http://archive.ambermd.org/202006/0130.html).
>
> Generated gb.mdout and pb.mdout files have:
> enb --> -nan
> eel --> -nan
>
> Does anyone know how to handle this problem?
>
> Kind regards,
>
> PhD Antonija Tomić
> LBPMM, Institut Ruđer Bošković
> Bijenička cesta 54, 10000 Zagreb, Croatia
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Oct 24 2022 - 05:00:02 PDT
