[AMBER] Questions about loading FF02 and MMGBSA

From: Matthew Guberman-Pfeffer <matthew.guberman-pfeffer.uconn.edu>
Date: Wed, 10 Feb 2021 21:40:46 -0500

Dear Amber Community,

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 /Users/XXX/opt/anaconda3/envs/AmberTools20/dat/leap/cmd/oldff/leaprc.ff02. However, when I load this file into leaprc, I get:

   PARM99 for DNA,RNA,AA, organic molecules, TIP3P wat. Polariz.& LP incl.02/04/99

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

This error message vanishes if I enter manually:

   loadamberparams parm99.dat
   loadamberparams frcmod.ff02pol.r1

However, if I then load a pdb, literally none of the residues are recognized. What am I missing or doing wrong?

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?

Best regards,
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Received on Wed Feb 10 2021 - 19:00:02 PST
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