Re: [AMBER] Resolving overlapping atoms.

From: David Case <>
Date: Thu, 9 Jan 2020 14:23:04 +0000

On Thu, Jan 09, 2020, Petro wrote:

>After adding water by addtobox to a pDB and ruining minimization I still
>have some overlapping water hydrogen. For now I came up with a crude
>solution and remove these 2-4 waters. But is there any way I can force
>minimization to solve it?

If you have bad initial water contacts, set ntmin=2 and run 500-1000
steps of minimization. That will just use Steepest descent, and will
avoid linmin problems.

However, I suspect that by asking for 100000 (!!) minimization steps,
you are just wasting computer time: does your energy not converge after
a few hundred steps?

>here is my minimization parameters :
>simple generalized Born minimization script
     (note that this is not a GB calculation)
> &cntrl
> imin=1, ! initiate minimization
> ntb=1, ! use NVT ensemble
> maxcyc=100000,
     (consider a value two to three orders of magnitude smaller)

> ntpr =10,
> cut=12.0, ! cutoff 12 Ang

This is way too big: stick with default of 8.

> ntr=1, ! weak positional restrains
> iwrap=1
>Keep protein fixed with weak restraints

   (these are actually fairly strong restriants: you protein atoms will
not move more that about 0.1 to 0.2 Ang, unless something is really

>The output of minimization repeatedly tells

This is expected: see above about not requesting so many minimization


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Received on Thu Jan 09 2020 - 06:30:03 PST
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