[AMBER] Yet again, MCPB.py for a ferrocene terminated monomer.

From: Gustaf Olsson <gustaf.olsson.lnu.se>
Date: Tue, 10 Aug 2021 13:58:27 +0000

After working through the tutorials, reading the MCPB.py paper and trying to replicate examples presented in the supporting information, I am no closer to manage to get MCPB.py to parse my files correctly.

I have tried changing and editing most things I could think of, residue names, numbers, adding/removing chain information, using pdb4amber, using AMBER atom types instead of GAFF and more things though still I cannot get MCPB.py to read anything but the FE iron ion.

   ***Selected Metal ion FE is atom 24 in residue 2-FE
   ***The following residues are in the Metal Site:
   Residue 2-FE
   ***The small model contains the following residues:
   ***The large model contains the following residues:

The only residue found/recognised is 2, the iron ion.

I have found indications of people working with ferrocene and MCPB.py (http://archive.ambermd.org/202001/0300.html) and have gotten indications from the developers that it should work and some useful tips. Sadly, as indicated MCPB.py does not seem to parse the files correctly.

As time is rapidly running out on producing something at all using this monomer I thought I’d just ask the forum in general for help. Therefore, to this email several files in a zip archive (ferrocene.zip) are attached. The archive contains the following:

   FE.mol2 The iron ion mol2 file prepared using metalpdb2mol2.py -i FE.pdb -o FE.mol2 -c 2
   FE.pdb The FE line extracted from the original PDB file (6SG)

   large.frcmod Antechamber produced FRCMOD file for the “larger” of the unsymmetrical metal binding parts part of the monomer
   large.mol2 mol2 file produced using antechamber (antechamber -fi pdb -fo mol2 -i large.pdb -o large.mol2 -c bcc -pf y -nc -1)
   large.pdb The lines containing the “large” portion cut from the “monomer.pdb"

   monomer.in MCPB.py input file with/without bond information (commented)

   monomer.pdb The monomer, derived from pdb 6SG, edited and minimised using avogadro to get the correct structure.

   small.frcmod FRCMOD file for the smaller of the unsymmetrical metal binding parts of the monomer as produced with antechamber
   small.mol2 mol2 file produced using antechamber (antechamber -fi pdb -fo mol2 -i small.pdb -o small.mol2 -c bcc -pf y -nc -1)
   small.pdb Lines containing the “small” portion cut from the “monomer.pdb"

My hope is that I am just missing something regarding the input, some piece of information somewhere that can get this to work as intended. In the MCPB.py input file are also ion-bond definitions which are commented out as the large/small files are not parsed correctly anyway.

Any help getting this to work or a confirmation that this will not work would be greatly appreciated.

Best regards
// Gustaf

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Received on Tue Aug 10 2021 - 07:00:02 PDT
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