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 <pratul.agarwal-lab.org>
wrote:
> 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 - 11:30:02 PST
