Re: [AMBER] Questions about loading FF02 and MMGBSA

From: David A Case <>
Date: Thu, 11 Feb 2021 07:42:14 -0500

On Wed, Feb 10, 2021, Matthew Guberman-Pfeffer wrote:
>Following the benchmarking of Phys. Chem. Chem. Phys., 2016, 18,
>22129 for protein-protein binding affinity, I want to set up MMGBSA
>calculations using ff02. I found what I think Is the relevant leaprc at
>AmberTools20/dat/leap/cmd/oldff/leaprc.ff02. However, when I load this file
>into leaprc, I get:

> /Users/XXX/opt/anaconda3/envs/AmberTools20/bin/teLeap: Fatal Error!
> Could not open file all_nucleic02.lib: not found

Change the reference in your leaprc file from "all_nucleic02.lib" to
>This error message vanishes if I enter manually:
> loadamberparams parm99.dat
> loadamberparams frcmod.ff02pol.r1

This looks like you want leaprc.ff02pol.r1, not leaprc.ff02. The latter is
*really* old, and the former is an updated version. Check the paper

>Finally, as I said, the goal is to do MMGBSA calculations. I ran a test
>calculation using ff14sb (before finding the benchmarking study mentioned
>above), and received a “bad atom name” message for FE; I’m looking at the
>association of heme proteins. Is the issue that no radius is defined for
>FE? How can I correct this, or whatever the problem may be?

Search the email archives for this: it comes up a lot.


AMBER mailing list
Received on Thu Feb 11 2021 - 05:00:02 PST
Custom Search