How long should the RESP fit step take?
My computer has been running at 90% CPU now for about 20 and the molecule is just a small metal-organic compound?
// Gustaf
> On 9 Jul 2021, at 11:12, Gustaf Olsson <gustaf.olsson.lnu.se> wrote:
>
> 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 - 08:00:02 PDT
