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

From: David A Case <>
Date: Wed, 16 Jan 2019 13:28:24 -0500

On Wed, Jan 16, 2019, Andrea H. Kasun wrote:
>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,
> 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
>RES 1 697
>But even with extra restraint, CL- ions (RESID 694 and 697) change their

Several points:

1. if you set restraintmask and restraint_wt, then the group restraints
(after the namelist) should be ignored.

2. You should look at the mdout file carefully: it will tell you how
many atoms are being restrained. Also see if you are getting a
non-zero restraint energy when the energies are printed. Make sure that
residues 694 and 697 are actually chlorides: these refer to "Amber"
residue numbers, not to the residue numbers the chlorides might have had
in the original structure.

3. If you "distances between protein ligand and CL ions ...
to stay unchanged", you should consider setting up internal distance
constraints (via nmropt=1) rather than absolute position restraints.

Having said that, I don't see anything wrong with your input; maybe
others on the list with better eyes will spot something.


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Received on Wed Jan 16 2019 - 10:30:03 PST
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