[AMBER] refene2.solvent_energies refene2.dielc2_energies and refene2.dielc2.solvent_energies

From: Luis Simon <lsimon.usal.es>
Date: Sun, 13 Dec 2020 00:03:01 +0100

Hello everyone,

I am trying to add some titratable groups following the Amber manual; I edited the tithable_residues.py file and cpinutil.py is able to create the .cpin files with the information on it. After using finddgref.py I can obtain a single energy correction term that I assume must be included in refene2 = _ReferenceEnergy(igb2=xxx, igb5=yyy, igb8=zzz) (xxx, yyy or zzzz depending on the igb value specified in the main file during finddgref.py execution). But what values should be used for refene1.solvent_energies refene1.dielc2_energies and refene1.dielc2.solvent_energies? It seems that these values are not printed in the STATENE in the cpin files… do they have any effect?

On the other hand, I obtain rather large values for the DELTAGREF (around 90-100 kcal/mol)… is this a reasonable result? I guess that it will depend on each case, but I wonder if such a large correction may indicate some fundamental mistake configuring some of the files.



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Received on Sat Dec 12 2020 - 15:30:02 PST
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