Which QM package did you use? What was the level of theory you applied? Was it DFT, HF or something more exotic? How big was your basis set?
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-----Original Message-----
From: Vaibhav Dixit <vaibhavadixit.gmail.com>
Sent: Friday, July 09, 2021 4:59 AM
To: AMBER Mailing List <amber.ambermd.org>
Subject: Re: [AMBER] MCPB.py tutorial issues
In my experience with MCBP.py tools, the QM calculation step took 2-4 days on Heme with nproc=16 and mem=45GB.
The frequency part of the calculation is usually the most time taking component.
It might be faster/slower if your system is smaller/larger, which depends on how many atoms you have in the "ligand+Ferrocene" system.
I hope that helps.
On Fri, Jul 9, 2021 at 2:15 PM Gustaf Olsson <gustaf.olsson.lnu.se> wrote:
> Apparently my question regarding ferrocene simulations may not have
> been of great general interest :)
>
> I did try and fail to construct a ferrocene terminated ligand from PDB
> according to the “examples” in "PCPB.py: A Python Based Metal Center”
> and as CSD was down, I could not check if the example presented would
> have worked either.
>
> I proceeded to try the tutorial to see if I could get anything to work
> and found some issues:
>
> -> metalpdb2mol2.py -i ZN.pdb -o mol2 ZN.mol2 -c 2
> should be:
> <- metalpdb2mol2.py -i ZN.pdb -o ZN.mol2 -c 2
>
> -> cat 1OKL_Hpp_fixed.pdb ZN.pdb MNS_H_fixed.pdb > 1OKL_H.pdb
> should be:
> <- cat 1OKL_Hpp_fixed.pdb ZN.pdb MNS_fixed_H.pdb > 1OKL_H.pdb
>
> Running
>
> pdb4amber -i 1OKL_H.pdb -o 1OKL_fixed_H.pdb
>
> Caused an error:
>
> Summary of pdb4amber for: 1OKL_H.pdb
> ===================================================
> Traceback (most recent call last):
> File "/Users/guolaa/SOFTWARE/amber20/bin/pdb4amber", line 33, in <module>
> sys.exit(load_entry_point('pdb4amber==20.1', 'console_scripts',
> 'pdb4amber')())
> File
> "/Users/guolaa/SOFTWARE/amber20/lib/python3.8/site-packages/./pdb4ambe
> r-20.1-py3.8.egg/pdb4amber/pdb4amber.py",
> line 816, in main
> run(
> File
> "/Users/guolaa/SOFTWARE/amber20/lib/python3.8/site-packages/./pdb4ambe
> r-20.1-py3.8.egg/pdb4amber/pdb4amber.py",
> line 520, in run
> pdbfixer._write_renum(base_filename)
> File
> "/Users/guolaa/SOFTWARE/amber20/lib/python3.8/site-packages/./pdb4ambe
> r-20.1-py3.8.egg/pdb4amber/pdb4amber.py",
> line 388, in _write_renum
> fh.write("%3s %c %5s %3s %5s\n" %
> TypeError: %c requires int or char
>
> Turns out that the provided 1OKL_Hpp_fixed.pdb file was the problem,
> there is no chain information (“A”) which seems to have been stripped
> by H++
>
> -> ATOM 1 N TRP 1 8.305 -0.472 10.466 1.00 0.00
> N
> should be:
> <- ATOM 1 N TRP A 1 8.305 -0.472 10.466 1.00 0.00
> N
>
> Adding the “A” back for every residue made the reference file work
> with pdb4amber.
>
> I am now considering using resources to perform the QM calculations, I
> see no estimate regarding the time needed to be invested in this step,
> or just use reference files to see what happens.
>
> // Gustaf
>
> > On 8 Jul 2021, at 10:52, Gustaf Olsson <gustaf.olsson.lnu.se> wrote:
> >
> > Like Christmas in July the good news arrived, I need a ferrocene
> containing/terminated monomer for MD simulations
> >
> > Like so many times before, metal-organic compounds is not my normal
> > area
> of interest and rather then trying to reinvent the wheel, I thought
> I’d ask the the community.
> >
> > Are there any recommendations/best practices regarding how to get up
> > and
> running quickly?
> >
> > I am really looking for the path of least resistance, preferably
> something with a written tutorial or at least well documented workflow
> if possible.
> >
> > I’ve seen MCPB.py mentioned a bunch of times. Could this be a
> > reasonable
> approach for some sort of ferrocene terminated alkene/carboxyl/acetyl
> structure. From the tutorials I saw the non bonder and dummy atom
> models as well.
> >
> > Thank you in advance and best regards // Gustaf
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
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>
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Received on Fri Jul 09 2021 - 12:00:04 PDT
