AMBER Archive (2007)

Subject: Re: AMBER: Charge not integral. Head-to-tail cyclic peptides

From: Melinda Layten (mlayten_at_gmail.com)
Date: Mon Jun 18 2007 - 09:28:57 CDT

The charges for the termini are distributed across the residue and removing
atoms is what is leaving you with the non-integer behavior.

Instead of modifying the charged termini, you may be better off deleting the
conversion to terminal residues in the leaprc file so that all of your
residues are the normal non-terminal residues. To do this copy the
leaprc.ff99SB (or whichever forcefield) to your local directory and
rename to just leaprc and remove the GLY -> CGLY and the SER -> NSER masks.
This will be loaded when tleap starts, just comment out your normal load
leaprc.XXX line

Hope this helps,

Melinda Layten

On 6/18/07, Giacomo Bastianelli <gbastian_at_pasteur.fr> wrote:
>
> Dear Amber users,
>
> I run Amber 9.0 on a Linux OS and I have been trying to
> run molecular dynamics on head-to-tail cyclic peptides.
> I have problems to balance the total charge of the protein.
>
> ERROR: The unperturbed charge of the unit: -1.594100 is not integral.
>
> Once I create the topology for the same peptide but linear,
> I then obtain a -2.000 protein total charge.
>
> Any suggestion on how to balance a not integral charge?
>
> Thanks,
>
> Giacomo
>
> ---
> Giacomo Bastianelli
> Ph.D fellow
> Structural Bioinformatics Unit
> Institut Pasteur
>
>
>
>
>
> ###COMMANDS###
>
> loadAmberParams parm99.dat
> MCOTI-II = loadPDB 1HA9_15_pfsub1.pdb
> desc MCOTI-II
> check MCOTI-II
> remove MCOTI-II MCOTI-II.1.H2
> remove MCOTI-II MCOTI-II.1.H3
> remove MCOTI-II MCOTI-II.34.OXT
> bond MCOTI-II.1.N MCOTI-II.34.C
> check MCOTI-II
> saveAmberParm MCOTI-II MCOTI-II.parm7 MCOTI-II.crd
> solvateOct MCOTI-II TIP3BOX 10
> charge MCOTI-II
> addIons2 MCOTI-II Na+ 2
> saveAmberParm MCOTI-II MCOTI-II.parm7 MCOTI-II.crd
>
>
> ###MESSAGES###
>
> Checking 'MCOTI-II'....
> ERROR: The unperturbed charge of the unit: -1.594100 is not integral.
> WARNING: The unperturbed charge of the unit: -1.594100 is not zero.
> Warning: Close contact of 1.353873 angstroms between .R<NSER 1>.A<H1 2>
> and .R<CGLY 34>.A<C 6>
> Checking parameters for unit 'MCOTI-II'.
> Checking for bond parameters.
> Checking for angle parameters.
> check: Errors: 1 Warnings: 2
> Checking Unit.
> ERROR: The unperturbed charge of the unit: -1.594100 is not integral.
> WARNING: The unperturbed charge of the unit: -1.594100 is not zero.
>
> -- ignoring the error and warning.
>
> Building topology.
> Building atom parameters.
> Building bond parameters.
> Building angle parameters.
> Building proper torsion parameters.
> Building improper torsion parameters.
> total 93 improper torsions applied
> Building H-Bond parameters.
> 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
>
> CGLY 1
> NSER 1
> )
> (no restraints)
> solvateOct: Argument #2 is type String must be of type: [unit]
> usage: solvateOct <solute> <solvent> <buffer> [aniso] [closeness]
> Total unperturbed charge: -1.594100
> Total perturbed charge: -1.594100
> Adding 2 counter ions to "MCOTI-II" using 1A grid
> Grid extends from solute vdw + 1.87 to 7.87
> Resolution: 1.00 Angstrom.
> grid build: 0 sec
> Calculating grid charges
> charges: 1 sec
> Placed Na+ in MCOTI-II at (-4.23, -9.65, 6.08).
> Placed Na+ in MCOTI-II at (7.77, 4.35, 3.08).
>
> Done adding ions.
> Checking Unit.
> ERROR: The unperturbed charge of the unit: 0.405900 is not integral.
> WARNING: The unperturbed charge of the unit: 0.405900 is not zero.
>
> -- ignoring the error and warning.
>
> Building topology.
> Building atom parameters.
> Building bond parameters.
> Building angle parameters.
> Building proper torsion parameters.
> Building improper torsion parameters.
> total 93 improper torsions applied
> Building H-Bond parameters.
> 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
>
> CGLY 1
> NSER 1
> )
> (no restraints)
>
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