Re: [AMBER] ATP and MG2+prep and frcmod files

From: Valentina Romano <>
Date: Thu, 14 Aug 2014 07:59:39 +0000

Can someone suggest a way to check if a molecule (like ATP) is well parametrized?

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

Phone: +41 61 267 15 80

From: Jason Swails []
Sent: Wednesday, August 13, 2014 6:21 PM
Subject: Re: [AMBER] ATP and MG2+prep and frcmod files

On Wed, 2014-08-13 at 15:28 +0000, Valentina Romano wrote:
> 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
> 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?

All it means is that no improper torsions were found for certain
collections of atoms. Improper torsions are usually used to ensure that
4 atoms remain planar. When a carbon atom is sp2-hybridized, it usually
forms a planar configuration with the 3 atoms that are attached to it.
So those 4 atoms are often fitted with an improper torsion to make sure
they stay planar.

tleap knows atom hybridization and can recognize situations where sp2
carbons exist. So all you are seeing here is a warning that tleap has
found what it expects should be planar regions but didn't see any
improper torsion parameters that fit those atom types. So it prints a
warning to that effect.

But improper torsions are not always needed to maintain planarity. So
this is just a warning, not an error. The only way to know if ATP is
well-parametrized is to test it. If the evidence given in the citation
accompanying the parameters is insufficient to convince you that the
parameters are good, you should conduct your own tests until you are

Hope this helps,

Jason M. Swails
Rutgers University
Postdoctoral Researcher
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Received on Thu Aug 14 2014 - 01:30:02 PDT
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