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)
Web: http://www.agarwal-lab.org/
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:
&cntrl
maxcyc=5000, imin=1, ntmin=1, ncyc=1000,
ntx=1,
igb=0, ntb=1, cut=10.0, dielc=1.0,
ntpr=10, nsnb=20,
ibelly=0, ntr=1, ntc=1, ntf=1,
drms=1e-3,
restraintmask=':253,692-697', restraint_wt=1000.0,
&end
restrained PROTEIN
100.0
RES 1 697
END
END
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,
Andrea
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Received on Wed Jan 16 2019 - 11:00:04 PST
