On Mon, May 12, 2014, Fengxue Li wrote:
> When doing nmode to calculate the entropy of my system, I get the
> nomde.out as follows:
> Root-mean-square gradient of input coords is 0.12566231540728257
> This is greater than the requested maximum: 1.00000000000000002E-003
Either the structure minimization you did was not thorough enough, or the
force field being used in nmode is different from that being used in sander
(or whatever program did the minimization).
I'm not familiar enough with mmpbsa.pl to grok what is happening here. But
you cannot just play around with drms: you have to figure out a way to get a
good minimum before trying to run normal modes.
...dac
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Received on Mon May 12 2014 - 05:00:04 PDT
