Sorry,
I meant How did you derive the partial charges?
Best Regards
Elvis Martis
Ph.D. Student (Computational Chemistry)
at Bombay College of Pharmacy
A Kalina, Santacruz [E], Mumbai 400098, INDIA
W www.elvismartis.in
Skype. adrian_elvis12
-----Original Message-----
From: Mrinal Arandhara [mailto:arandharamrinal.gmail.com]
Sent: Sunday, March 05, 2017 8:51 PM
To: amber.ambermd.org
Subject: [AMBER] dUMP parameters
I'm trying to run a MD simulation of protien-ligand complex with
dUMP(monoanionic) as cofactor. The gaff parameters for dUMP generated by parmchk has reasonable penalty values but after minimisation step two atoms(one O and the other hydroxyl-H) attached to the P-atom are sitting on top of each other and 1-4 EEL value is very large (*************) .Is it due to wrong force field parameters or wrong charges ??Are the parameters for dUMP available ??
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Received on Sun Mar 05 2017 - 08:00:03 PST
