Dear Amber users,
To parametrize a complex of a kinase bound to ATP and 2 Mg2+ ions, I used the ATP.prep and frcmod.phos available on
http://www.pharmacy.manchester.ac.uk/bryce/amber/
The input file was:
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
Analyzing the leap.log files, I noticed the following messages:
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
total 762 improper torsions applied
5 improper torsions in old prep form
Building H-Bond parameters.
Incorporating Non-Bonded adjustments.
Not Marking per-residue atom chain types.
Marking per-residue atom chain types.
(Residues lacking connect0/connect1 -
these don't have chain types marked:
res total affected
CLEU 1
NTYR 1
WAT 8236
)
(no restraints)
> quit
Quit
I am wondering that the ATP is not well parametrized.
Can anyone help me to understand what was happened?
Thank you,
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 Wed Aug 13 2014 - 09:00:02 PDT
