[AMBER] Combining MCPB.py results using tleap

From: Anthony Nash <anthony.nash.ndcn.ox.ac.uk>
Date: Wed, 18 Aug 2021 19:12:55 +0000

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

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

Kind regards
Dr Anthony Nash PhD MRSC

Senior Research Scientist
Nuffield Department of Clinical Neurosciences
RMCR Kellogg College
University of Oxford

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Received on Wed Aug 18 2021 - 12:30:02 PDT
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