[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
Sam

University of Huddersfield inspiring global professionals.
[http://marketing.hud.ac.uk/_HOSTED/EmailSig2014/EmailSigFooterMarch2019.jpg]

This transmission is confidential and may be legally privileged. If you receive it in error, please notify us immediately by e-mail and remove it from your system. If the content of this e-mail does not relate to the business of the University of Huddersfield, then we do not endorse it and will accept no liability.
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Feb 12 2021 - 14:00:02 PST
Custom Search