[AMBER] Using divalent ions in LEaP

From: Sam Walsworth (Researcher) <"Sam>
Date: Fri, 12 Feb 2021 21:30:36 +0000

Hello all

I'm trying to run simulations of a protein that has a zinc 2+ cofactor. The amber manual mentions you can use relevant frcmod files for di/tri/tetravalent ions (e.g. frcmod.ions234lm_126_tip3p has Zn2+ parameters to be used with tip3p, the frcmod file I'm interested in). The problem is LEaP doesn't recognise the Zn2+ species in my pdb file (for some reason the + in Zn2+ seems to be omitted when read from a PDB file so I called my zinc ion Zn2 in the PDB and renamed the Zn2+ in the frcmod to Zn2 to try make them match):

> MPI = loadpdb mpi_noligand.pdb
Warning: Unknown residue: Zn2....
..relaxing end constraints to find a dbase match

Warning: -no luck

# Proceeds to create Zn residue, so I tried to load in the frcmod in question

> loadamberparams frcmod.ions234lm_126_tip3p
Loading parameters: ./frcmod.ions234lm_126_tip3p
> check MPI
FATAL : Atom .R<Zn2 442>.A<Zn2 1> does not have a type.

I'm not sure if I'm misunderstanding the amber manual and I'm trying to load the wrong file (or that I need to load an additional file) or if I'm simply getting something more basic wrong like formatting/doing things in the wrong order etc.

Thanks in advance

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Received on Fri Feb 12 2021 - 14:00:02 PST
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