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

From: Pratul Agarwal <>
Date: Wed, 16 Jan 2019 19:09:53 +0000

Okay. Thank you for the information. You should definitely check the things Dave suggested to make sure that the restraints are being read in properly and being applied.

However is it possible that your ions are staying in place and other atoms are moving? This would change the distances between the atoms. Perhaps make a movie of multiple frames and see if the ion stay in place (you will need to RMS fit all frames to a common frame though).

Alternatively, if your goal is to keep distance(s) fixed then you could also apply distance restraints (nmropt keyword) instead of positional restraints. Just a suggestion.

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

On 1/16/2019 2:02 PM, Andrea H. Kasun wrote:

Thank you for your answers and suggestions!
I generated PDB file from RST output file (with ambpdb program) and then
measured the distances between atoms in VMD program.

On Wed, Jan 16, 2019 at 7:49 PM Pratul Agarwal <><>

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 - 11:30:03 PST
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