Hi,
I am running entropy for protein-ligand complex using NMODE. I got the
deltaS result, but it shows the below message while running the job. I get
the same message, even i try with single frame or many frames. Is the
result acceptable? I have seen the previous amberlist responses, they said
that minimization is getting stuck. How to overcome this? Do we need to run
many minimization steps before running MD?
Line minimizer aborted: step at upper bound 0.0020765772
Line minimizer aborted: step at upper bound 0.0018317604
Line minimizer aborted: step at upper bound 0.0015270612
Line minimizer aborted: step at upper bound 0.047828871
Line minimizer aborted: step at upper bound 0.030144341
Line minimizer aborted: step at upper bound 0.12217309
Input file for running entropy calculations using NMode
&general
endframe=10000, keep_files=2,
/
&nmode
nmstartframe=9999, nmendframe=10000,
nminterval=1, nmode_igb=1, nmode_istrng=0.1,
/
P.S. I am running the MD simulations in AMBER16 using pmemd.cuda.
Best Regards,
KK
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Received on Fri Mar 17 2017 - 09:30:02 PDT
