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
quit
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.
Best,
Valentina
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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
