Hi Sarah,
That's perfect. Thank you for your swift response.
Thanks
Anthony
Kind regards
Dr Anthony Nash PhD MRSC
Senior Research Scientist
Nuffield Department of Clinical Neurosciences
RMCR Kellogg College
University of Oxford
http://www.kellogg.ox.ac.uk/
________________________________
From: Sarah Lefave <s.lefave.utah.edu>
Sent: 18 August 2021 20:59
To: AMBER Mailing List <amber.ambermd.org>
Subject: Re: [AMBER] [UCE] Combining MCPB.py results using tleap
Hi Anthony,
Without doing a deep and thorough look through your files I can suggest a few things that helped me (I parameterized a 3 metal active site with one normal heme ligand and two that were more in the non-standard category).
Anyway, in my experience, every parameterized “metal site” named the metal M1 and connectors Y1, Y2, etc. However, those can only have one set of forces and parameters that define them or there are tons of problems with connections, angles, forces, etc. So, each atom that has a force modification (anything that isn’t a standard amino acid atom must have a unique name. You will likely need to rename metals to have M1 - M6 and various Y’s ( I also think you cannot go beyond Y9 so maybe try YA but I could be mistaken). Additionally, this needs to be consistent throughout every modification file (mol2, frcmod, and master.pdb). It was certainly tedious in my experience but eventually was able to successfully finish all the syntaxing challenges and move on to actual MD.
Hope this is helpful or can at least point you in the right direction!
Sarah
> On Aug 18, 2021, at 1:12 PM, Anthony Nash <anthony.nash.ndcn.ox.ac.uk> wrote:
>
> Hi all,
>
> A long time MD user, but with close to zero Amber experience.
>
> Using MCPB.py and GAMESS-US, I've derived the force constants for 6 metal ions and their corresponding ligand side chains. I've got all the way to have 6 unique .pdb, .prmtop, .inpcrd along with all the mol2 and frcmod files.
>
> The problem I now have is combining the six sets of topology data into one (recap: 6 metals, 6 directories, 6 complete sets of files).
>
> I don't quite know how to do this using tleap. So, putting files and my experience together, I decided to keep one "master.pdb" file, rename all the affected residue names e.g., residue HE1.mol2 to Z1A .mol2(for the first of two zincs and the first ligand(A)) and propagate those through the master.pdb. Long story short, I will have renamed around 30 residues so they match the mol2 files.
>
> I thought this would work. In truth, I don't know how this is going to affect reading in the frcmod files.
>
> My merged tleap input file (just merged both zinc data sets as a test) contains:
>
> source oldff/leaprc.ff99
> source leaprc.gaff
> source leaprc.water.opc
> addAtomTypes {
> { "M1" "Zn" "sp3" }
> { "Y1" "N" "sp3" }
> { "Y2" "O" "sp3" }
> { "Y3" "N" "sp3" }
> { "Y4" "N" "sp3" }
> }
> Z1A = loadmol2 Z1A.mol2
> Z1B = loadmol2 Z1B.mol2
> Z1C = loadmol2 Z1C.mol2
> Z1D = loadmol2 Z1D.mol2
> Z1E = loadmol2 Z1E.mol2
>
> Z2A = loadmol2 Z2A.mol2
> Z2B = loadmol2 Z2B.mol2
> Z2C = loadmol2 Z2C.mol2
> Z2D = loadmol2 Z2D.mol2
>
>
> loadamberparams frcmod.ionslm_126_opc
> loadamberparams MMP1_zn_1201_mcpbpy.frcmod
> loadamberparams MMP1_zn_1202_mcpbpy.frcmod
> mol = loadpdb adjusted.pdb
> bond mol.179.SG mol.367.SG
> bond mol.69.NE2 mol.368.ZN
> bond mol.71.OD2 mol.368.ZN
> bond mol.84.NE2 mol.368.ZN
> bond mol.97.ND1 mol.368.ZN
> bond mol.68.C mol.69.N
> bond mol.69.C mol.70.N
> bond mol.70.C mol.71.N
> bond mol.71.C mol.72.N
> bond mol.83.C mol.84.N
> bond mol.84.C mol.85.N
> bond mol.96.C mol.97.N
> bond mol.97.C mol.98.N
>
> bond mol.119.NE2 mol.368.ZN
> bond mol.123.NE2 mol.368.ZN
> bond mol.129.NE2 mol.368.ZN
> bond mol.118.C mol.119.N
> bond mol.119.C mol.120.N
> bond mol.122.C mol.123.N
> bond mol.123.C mol.124.N
> bond mol.128.C mol.129.N
> bond mol.129.C mol.130.N
>
>
> savepdb mol combined_dry.pdb
> saveamberparm mol combined.prmtop combined.inpcrd
> solvatebox mol OPCBOX 10.0
> addions mol Na+ 0
> addions mol Cl- 0
> savepdb mol combined_solv.pdb
> saveamberparm mol combined_solv.prmtop combined_solv.inpcrd
> quit
>
>
> I see lots of these warnings:
>
> /home/ubuntu/miniconda3/envs/AmberTools21/bin/teLeap: Warning!
> One sided connection. Residue (Z1A) missing connect0 atom.
>
>
> And then loads of these errors:
>
> Building topology.
> Building atom parameters.
> Building bond parameters.
> Building angle parameters.
>
> /home/ubuntu/miniconda3/envs/AmberTools21/bin/teLeap: Error!
> Could not find angle parameter: Y1 - M1 - Y1
>
> /home/ubuntu/miniconda3/envs/AmberTools21/bin/teLeap: Error!
> Could not find angle parameter: Y2 - M1 - Y2
>
> /home/ubuntu/miniconda3/envs/AmberTools21/bin/teLeap: Error!
> Could not find angle parameter: Y3 - M1 - Y3
> Building proper torsion parameters.
>
> /home/ubuntu/miniconda3/envs/AmberTools21/bin/teLeap: Error!
> ** No torsion terms for CV-Y1-M1-Y1
>
>
> I could hack away, but I've spent hours finally getting the force constant data. Now, combining them into one topology involves me holding my hands up for a bit and hoping those with more experience can help.
>
> Many thanks
> Anthony
>
>
>
>
> Kind regards
> Dr Anthony Nash PhD MRSC
>
> Senior Research Scientist
> Nuffield Department of Clinical Neurosciences
> RMCR Kellogg College
> University of Oxford
> http://www.kellogg.ox.ac.uk/
>
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Received on Wed Aug 18 2021 - 13:30:03 PDT
