Re: [AMBER] Using divalent ions in LEaP

From: Sam Walsworth (Researcher) <"Sam>
Date: Fri, 12 Feb 2021 22:04:26 +0000

Hi Maria

I can't find a .lib file that contains Zn2+, only a series of .frcmod files that do.

From: Maria Nagan <>
Sent: 12 February 2021 21:45
To: AMBER Mailing List <>
Subject: Re: [AMBER] Using divalent ions in LEaP

Dear Sam,

You need the exact name in your pdb file to match the name in the lib file and frcmod file.

The general order is to:
load lib files for all your molecules (e.g. protein, ions, water)
This tells Amber what your residues names, atoms, etc. are called and your charges
load frcmod files for all your molecules (e.g. protein, ions, water)
This tells Amber what your atom types, force constants, etc. are called
load your pdb file
Parameters are listed on the Amber website under “Force Fields”;;sdata=KCm34gev0fWfT4sgDwTeT%2BYDz%2FoFUbyBau38CtiKlcc%3D&amp;reserved=0

lib files can be also found under:

frcmod files can be also found under:

You should make sure your pdb file residue names match your lib file residue names. You are missing Zn2+ cation parameters.


> On Feb 12, 2021, at 4:30 PM, Sam Walsworth (Researcher) <> wrote:
> 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
> Sam
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Received on Fri Feb 12 2021 - 14:30:02 PST
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