[AMBER] MCPB.py tutorial issues

From: Gustaf Olsson <gustaf.olsson.lnu.se>
Date: Fri, 9 Jul 2021 08:45:14 +0000

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


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
 File "/Users/guolaa/SOFTWARE/amber20/lib/python3.8/site-packages/./pdb4amber-20.1-py3.8.egg/pdb4amber/pdb4amber.py", line 520, in run
 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 - 02:00:02 PDT
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