Re: [AMBER] How to perform Newton-Raphson minimization to protein

From: David A Case <>
Date: Tue, 23 Jan 2018 08:26:46 -0500

On Tue, Jan 23, 2018, 巩梦雪 wrote:

> When I used the Newton-Raphson method to optimize the protein, I got the following error :
> ××××××××××××××××××××××××××××××××××××××××××××××××××××
> Reading parm file (1h22_10.prmtop)
> title:
> default_name
> Parameter topology includes 10-12 terms:
> These are assumed to be zero here (e.g. from TIP3P water)

This is unusual: do you know why you have 10-12 terms in the prmtop file?
How did you create this file?

> The reason for the optimization failure is not known because the
> optimized protein is too large or not enough memory.

How many atoms are in your simulation? The Newton-Raphson method takes *lots*
of memory, which you might not have.

Note that it is rarely necessary to use this method: if you are patient, xmin
minimization can take you to a very low gradient, and requires much less


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Received on Tue Jan 23 2018 - 05:30:02 PST
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