I love to see late night (or early morning european) work for amber! I do not think there was any change in MASS. CI was a new atom type for the nucleic acid force field in the backbone for the parmbsc0 to avoid issues with bad alpha/gamma transitions to g+/t. If there is a real warning, beyond that for normal force field, let us know... However, I think the mass of carbon atoms has not changed in recent years.
--tec3
________________________________________
From: Alan <alanwilter.gmail.com>
Sent: Saturday, February 6, 2021 1:12:55 AM
To: AMBER Mailing List
Subject: [AMBER] About changes in frcmod.parmbsc0
I'm reviewing my old tutorials, trying to update them, if possible, and
came across an enigmatic comment I did several years ago:
$AMBERHOME/dat/leap/parm/frcmod.parmbsc0: fixed CI mass to 12.01
I'm wondering what was the old value and when that change happened because
I can see in AmberTools20 this is now CI mass 12.01, see:
head $AMBERHOME/dat/leap/parm/frcmod.parmbsc0
modifies parm99 for nucleic acids: see http://mmb.pcb.ub.es/PARMBSC0/
MASS
CI 12.01
BOND
CI-H1 340.0 1.090
...
BTW, I know BSC0 was not developed by Amber but link
http://mmb.pcb.ub.es/PARMBSC0/ is not alive anymore.
Thanks in advance,
--
Alan Silva
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Received on Sat Feb 06 2021 - 00:30:03 PST
