I apologize if I didn't understand well. Are you suggesting to try to
remove EPW particle ("extra point") from top and crd files? If I remove
them what about its charge? What about electrostatic interaction
calculations?
Thank you in advance for your reply,
Antonija
Dana 2022-10-24 13:51, Carlos Simmerling je napisao(la):
> 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
>>
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>> http://lists.ambermd.org/mailman/listinfo/amber
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Received on Mon Oct 24 2022 - 07:30:02 PDT
