Re: [AMBER] Kinase and ATP MD simulation

From: Jason Swails <>
Date: Thu, 14 Aug 2014 12:18:49 -0400

On Thu, 2014-08-14 at 15:49 +0000, Valentina Romano wrote:
> Dear Amber users
> I ran a 30ns MD for a kinase protein in complex with ATP and 2 Mg2+ ions.
> After a few ns, The ATP moved away from the protein binding site and this is not correct.
> I am wondering that this behavior depends on a wrong parametrization.

That's quite possible. It's also possible that the original binding
pose was not favorable enough to stabilize binding. Either case
requires investigation.

> To parametrize the whole complex (protein, ligand, and ions), I used the following file:
> source leaprc.ff99SB
> loadamberparams frcmod.phos
> loadamberprep ATP.prep
> COMPLEX = loadpdb PknGATP_init_min_vac.pdb
> alignAxes COMPLEX
> addions COMPLEX Na+ 6
> solvatebox COMPLEX TIP3PBOX 8.0
> saveamberparm COMPLEX PknGATP_wt.prmtop PknGATP_wt.inpcrd
> quit

I would suggest using the most up-to-date ion parameters possible. See
chapter 3 section 9 of the AmberTools 14 manual that talks about the
latest ion parameters. In particular, you will need to use the ion
parameters that are compatible with the water model you're using (in
this case, TIP3PBOX). Also, 8 Angstrom buffer is awfully small... Are
you sure that your system is not interacting with periodic images (it is
especially problematic when using solvateBox when your system is
particularly long in one dimension).
> The leap.log file contained the following warning:
> Checking Unit.
> Building topology.
> Building atom parameters.
> Building bond parameters.
> Building angle parameters.
> Building proper torsion parameters.
> Building improper torsion parameters.
> ** Warning: No sp2 improper torsion term for C*-CN-CB-CA
> atoms are: CG CE2 CD2 CE3
> ** Warning: No sp2 improper torsion term for NA-CA-CN-CB
> atoms are: NE1 CZ2 CE2 CD2
> ** Warning: No sp2 improper torsion term for NC-CB-CB-N*
> atoms are: N3 C5 C4 N9
> ** Warning: No sp2 improper torsion term for NB-CA-CB-CB
> atoms are: N7 C6 C5 C4
> old PREP-specified impropers:
> <ATP 247>: C8 C4 N9 C1*
> <ATP 247>: C6 H60 N6 H61
> <ATP 247>: N7 N9 C8 H80
> <ATP 247>: N1 N3 C2 H2
> <ATP 247>: C5 N1 C6 N6
> Do you think there is a relation between the warning message and the wrong behavior of the ATP during the MD?

No. It's not impossible, but the likelihood is very low that missing
impropers (which would only lead to molecules that aren't as planar as
they should be) pushes a ligand out of the binding pocket.

> Do you have any suggestion to understand what happened?

Unless there are strong interactions between the ligand and the binding
pocket, or some flap has 'closed' over the opening after binding, or
maybe the ligand is not soluble in water, then entropy will drive the
ligand to leave the pocket. The fact that the ligand resides in the
pocket for a few nanoseconds before drifting out suggests that there
isn't a strong repulsive force _pushing_ the ligand out, but rather that
the attractive force is too weak to hold it in for a long time.

Watch your trajectory, paying careful attention to polar and nonpolar
contacts between the ligand and the binding pocket. Is water displacing
the charged groups of your ATP? Is there a conformational change in the
binding pocket that may be driving the ligand out?

These are the types of questions you should be asking yourself when you
investigate what happened and why it happened.

Hope this helps,

Jason M. Swails
Rutgers University
Postdoctoral Researcher
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Received on Thu Aug 14 2014 - 09:30:02 PDT
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