Hello
I have been trying to neutralize my system whic has a non-standard base
with Na+ ions.
The command is given as shown below:
addions rna Na+ 0
5 Na+ ions required to neutralize.
Adding 5 counter ions to "rna" using 1A grid
Grid extends from solute vdw + 1.87 to 7.97
Resolution: 1.00 Angstrom.
grid build: 0 sec
(no solvent present)
Calculating grid charges
charges: 1 sec
Placed Na+ in rna at (-5.09, 4.27, -1.53).
Placed Na+ in rna at (-1.09, 9.27,-5.53).
Placed Na+ in rna at (7.91, -4.73, 11.47).
Placed Na+ in rna at (-7.09, 5.27, 9.47).
Placed Na+ in rna at (-2.09, 2.27, 1.47).
Done adding ions.
To build the parameter topology file :
saveamberparm rna rna_cio.prmtop rna_cio.inpcrd
Checking Unit.
ERROR:The unperturbed charge of the unit: -0.691900 is not integral.
WARNING: The unperturbed charge of the unit: -0.691900 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.
old PREP-specified impropers:
total 37 improper torsions applied
0 improper torsions in old prep form
Building H-Bond parameters.
Not Marking per-residue atom chain types.
Marking per-residue atom chain types.
(no restraints)
Despite adding the Na ions the charge is not integral. When I use a
standard base the whole system gets neutralizes. Is it due to the presence
of a non-standard base?
Thank You
Martina
Research Scholar
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Received on Tue Aug 25 2015 - 00:00:02 PDT
