Hi Gustaf,
The coordinate bonds for the ferrocene system are Fe-Carbon bonds. By default MCPB.py will not recognize the metal-carbon bonds. To make it be able to recognize these bonds, you can check the page 333 in the AMBER manual about the add_bonded_pairs variable: https://ambermd.org/doc12/Amber21.pdf <https://ambermd.org/doc12/Amber20.pdf>.
Moreover, based on my experience, the pdb4amber in AMBER 2021 does not work well for some systems, while the pdb4amber in AMBER 2020 can work for these systems.
The Merz-Kollman population analysis usually takes some time to finish. However, the RESP fit based on the Gaussian log file of the Merz-Kollman population analysis should be pretty quick.
Hope it helps,
Pengfei
> On Jul 9, 2021, at 9:54 AM, Gustaf Olsson <gustaf.olsson.lnu.se> wrote:
>
> 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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>>>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>>
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Received on Tue Jul 13 2021 - 20:00:03 PDT
