[AMBER] ATP and MG2+prep and frcmod files

From: Valentina Romano <valentina.romano.unibas.ch>
Date: Wed, 13 Aug 2014 15:28:27 +0000

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

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

I am wondering that the ATP is not well parametrized.
Can anyone help me to understand what was 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 Wed Aug 13 2014 - 09:00:02 PDT
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