Dear Amber Users,
I am trying to simulate a MD system where the protein bound to
guanosine-diphosphate-monothiophostate (GSP).
I generated the GSP parameters using GAFF and build the system with tleap.
The minimization procedure ran without any error.
The problem occurs when I moved the system to MD runs.
The writing the files for every steps shows that phosphate and sulphur
group overlap each other and the simulation crashes.
Could you please advice to get parameters for thiophosphate group
Thank You,
Balaji
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Received on Wed Feb 01 2017 - 11:00:02 PST
