Thank you, it does.
As my entire structure is basically the ferrocene terminated ligand, then it should be a lot faster than the HEME or 1OKL examples presented.
Best regards
// Gustaf
> On 9 Jul 2021, at 10:58, Vaibhav Dixit <vaibhavadixit.gmail.com> wrote:
>
> 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/./pdb4amber-20.1-py3.8.egg/pdb4amber/pdb4amber.py",
>> line 816, in main
>> run(
>> File
>> "/Users/guolaa/SOFTWARE/amber20/lib/python3.8/site-packages/./pdb4amber-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/./pdb4amber-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
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Received on Fri Jul 09 2021 - 02:30:03 PDT
