[AMBER] Kinase and ATP MD simulation

From: Valentina Romano <valentina.romano.unibas.ch>
Date: Thu, 14 Aug 2014 15:49:45 +0000

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.
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

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?
Do you have any suggestion to understand what happened?

Thank you.


Valentina Romano | PhD Student | Biozentrum, University of Basel & SIB Swiss Institute of Bioinformatics
Klingelbergstrasse 61 | CH-4056 Basel |

Phone: +41 61 267 15 80

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Received on Thu Aug 14 2014 - 09:00:03 PDT
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