Re: [AMBER] nmode entropy calculations gets stuck way too often

From: Liao <>
Date: Sat, 4 Apr 2020 14:26:25 -0500

Thanks there, I can look into the by hand minimization method.
The system is in total 261 residues, 2 proteins and a ligand.
I was also planning to change drms to a larger value like 0.005 or 0.01, to see if the entropy values differ greatly than compared to 0.002 that I was using. If the values are close enough it can also be a solution.

Sent from my iPhone

> On Apr 4, 2020, at 12:30 PM, David A Case <> wrote:
> On Fri, Apr 03, 2020, Liao wrote:
>> With drms=0.002, maxcyc=1000, I can see that in the nm.out file that gets
>> stuck (usually stuck already by 200ns), the RMSG will go back and forth
>> between a certain value, and never reach the drms value set. Whether
>> maxcyc=1000 or 10000 doesn’t help, it usually gets stuck by iteration 200
>> or so.
> This is a case where you may need to do the entropy part "by hand". I'd
> explore using txmin.c to carry out the minimization, and tnmode.c to do
> the subsequent normal mode analysis. (These programs are in
> AmberTools/test/nabc; you can also use NAB versions of the same thing.)
> Be sure you have SHAKE turned off in the minimization.
> Equally well, you can modify the sander minimization to use xmin (set
> ntmin=3).
> Caveat: I'm not familiar with how many options you have in using the
> scripts -- there may be option there that others on the list
> can suggest.
> It would help to know how big your system is.
> ...thx...dac
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Received on Sat Apr 04 2020 - 12:30:02 PDT
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