On Fri, Apr 24, 2026, ElBagoury, Abdulrahman Walid Attia Ibrahim via AMBER wrote:
>so what could be your recommendation ? is there a way to adjust for the close contacts ?
Don't be afraid to experiment. A short (say 100 step) minimization using
sander with ntmin=3 and some constraints (ntr=1) on non-hydrogen atoms
should tell you a lot.
Aside to all users: using sander with ntmin=3 is generally the best approach
for minimization, unless you have some known reason to avoid it. (Let us
know details if this fails where some other option is OK.)
....dac
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Received on Fri Apr 24 2026 - 14:00:02 PDT
