AMBER Archive (2007)

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

From: Giacomo Bastianelli (gbastian_at_pasteur.fr)
Date: Mon Jun 18 2007 - 08:55:46 CDT

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)

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu