Re: [AMBER] Can't put position restrains on ions

From: Pratul Agarwal <>
Date: Wed, 16 Jan 2019 18:49:26 +0000

This is interesting. I also don't see anything wrong with the input either.

With a value of 1000, they shouldn't be moving much at all. How did you determine they are moving?

Pratul K. Agarwal, Ph.D.
(Editorial Board Member: PLoS ONE, Microbial Cell Factories)

On 1/16/2019 10:33 AM, Andrea H. Kasun wrote:

Dear Amber users,

I need to fixate CL ions which are specifically positioned near the
protein ligand, and this distances between protein ligand and CL ions need
to stay unchanged trough all MD simulation.
I tried to run first cycle of minimization with this input file:
    maxcyc=5000, imin=1, ntmin=1, ncyc=1000,
    igb=0, ntb=1, cut=10.0, dielc=1.0,
    ntpr=10, nsnb=20,
    ibelly=0, ntr=1, ntc=1, ntf=1,
    restraintmask=':253,692-697', restraint_wt=1000.0,
restrained PROTEIN
RES 1 697
But even with extra restraint, CL- ions (RESID 694 and 697) change their
positions. With every other cycle of minimisation the distance is getting
bigger and bigger. I tried to increase restraint_wt to 10000 but the
distance continues to change... Can you please give me advice how to fixate
this ions? I don't want to use ibelly option because of its incompatibility
with GPU.

Thank you in advance,
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Received on Wed Jan 16 2019 - 11:00:04 PST
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