Re: [AMBER] restraint 10 kcal/mol

From: David A Case <>
Date: Wed, 24 Jun 2020 21:36:37 -0400

On Wed, Jun 24, 2020, Debarati DasGupta wrote:

> ntr=1, restraintmask=':EOH', restraint_wt=10.00,

Note this will keep the EOH residue from moving, but all other parts of
the simulation are free to go where they wish. This doesn't keep the
ligand "in the pocket"; it just keeps the xyz coordinates of the EOH
atoms near their starting point. Basically, all this will do is to
ensure that internal geometry of EOH is kept fixed. I doubt that is
really what you wanted to do: since ethanol is rather rigid anyway, this
is almost like having no restraint at all.

>So, after the run was complete, I was curious to see how far my ligand
>has translated from its tether point.. and after doing a COM distance
>cpptraj script run, I find that for 3 lambda values 0.11505, 0.20634,
>and 0.31608; the ligand has moved around quite a bit as in > 3 Angstroms

It's not at all clear what you mean by a "COM distance cpptraj script";
but I hope the explanation of the restraint mask above will help.


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Received on Wed Jun 24 2020 - 19:00:03 PDT
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