Dear Amber Users and Developers,
I am going
to simulate a CNT functionalized with HIP by AMBER12 using ff12SB. I have a
off file of it. After loading the off file and pdb file of my system I
solvate it by about 5000 TIP3P water molecules. Then add one Cl- ion to
neutralize the system. Now when I am going to make prmtop and inpcrd file,I
am getting following warnings.
> saveamberparm cnt cnt_hip1.prmtop cnt_hip1.inpcrd
Checking Unit.
Building topology.
Building atom parameters.
Building bond parameters.
Building angle parameters.
Building proper torsion parameters.
Building improper torsion parameters.
total 0 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
WAT 4894
cnt 1
)
(no restraints)
WARNING: Unbonded Hydrogen atom HE2 in cnt.
Cannot determine the requested GB radius for this atom.
Writing the unmodified Bondi GB radius.
WARNING: Unbonded Hydrogen atom HE1 in cnt.
Cannot determine the requested GB radius for this atom.
Writing the unmodified Bondi GB radius.
WARNING: Unbonded Hydrogen atom HD1 in cnt.
Cannot determine the requested GB radius for this atom.
Writing the unmodified Bondi GB radius.
WARNING: Unbonded Hydrogen atom HD2 in cnt.
Cannot determine the requested GB radius for this atom.
Writing the unmodified Bondi GB radius.
WARNING: Unbonded Hydrogen atom HB1 in cnt.
Cannot determine the requested GB radius for this atom.
Writing the unmodified Bondi GB radius.
WARNING: Unbonded Hydrogen atom HB2 in cnt.
Cannot determine the requested GB radius for this atom.
Writing the unmodified Bondi GB radius.
WARNING: Unbonded Hydrogen atom H1 in cnt.
Cannot determine the requested GB radius for this atom.
Writing the unmodified Bondi GB radius.
WARNING: Unbonded Hydrogen atom H2 in cnt.
Cannot determine the requested GB radius for this atom.
Writing the unmodified Bondi GB radius.
WARNING: Unbonded Hydrogen atom H3 in cnt.
Cannot determine the requested GB radius for this atom.
Writing the unmodified Bondi GB radius.
WARNING: Unbonded Hydrogen atom H4 in cnt.
Cannot determine the requested GB radius for this atom.
Writing the unmodified Bondi GB radius.
WARNING: Unbonded Hydrogen atom H5 in cnt.
Cannot determine the requested GB radius for this atom.
Writing the unmodified Bondi GB radius.
WARNING: Unbonded Hydrogen atom H6 in cnt.
Cannot determine the requested GB radius for this atom.
WARNING: Unbonded Hydrogen atom H7 in cnt.
Cannot determine the requested GB radius for this atom.
Writing the unmodified Bondi GB radius.
WARNING: Unbonded Hydrogen atom H8 in cnt.
Cannot determine the requested GB radius for this atom.
Writing the unmodified Bondi GB radius.
WARNING: Unbonded Hydrogen atom H9 in cnt.
Cannot determine the requested GB radius for this atom.
Writing the unmodified Bondi GB radius.
WARNING: Unbonded Hydrogen atom H10 in cnt.
Cannot determine the requested GB radius for this atom.
Writing the unmodified Bondi GB radius.
WARNING: Unbonded Hydrogen atom H11 in cnt.
Cannot determine the requested GB radius for this atom.
Writing the unmodified Bondi GB radius.
WARNING: Unbonded Hydrogen atom H12 in cnt.
Cannot determine the requested GB radius for this atom.
Writing the unmodified Bondi GB radius.
WARNING: Unbonded Hydrogen atom H13 in cnt.
Cannot determine the requested GB radius for this atom.
Writing the unmodified Bondi GB radius.
WARNING: Unbonded Hydrogen atom H14 in cnt.
Cannot determine the requested GB radius for this atom.
Writing the unmodified Bondi GB radius.
WARNING: Unbonded Hydrogen atom H15 in cnt.
Cannot determine the requested GB radius for this atom.
Writing the unmodified Bondi GB radius.
WARNING: Unbonded Hydrogen atom H16 in cnt.
Cannot determine the requested GB radius for this atom.
Writing the unmodified Bondi GB radius.
WARNING: Unbonded Hydrogen atom H17 in cnt.
Cannot determine the requested GB radius for this atom.
Writing the unmodified Bondi GB radius.
WARNING: Unbonded Hydrogen atom H18 in cnt.
Cannot determine the requested GB radius for this atom.
Writing the unmodified Bondi GB radius.
WARNING: Unbonded Hydrogen atom H19 in cnt.
Cannot determine the requested GB radius for this atom.
Writing the unmodified Bondi GB radius.
WARNING: Unbonded Hydrogen atom H20 in cnt.
Cannot determine the requested GB radius for this atom.
Writing the unmodified Bondi GB radius.
WARNING: Unbonded Hydrogen atom H21 in cnt.
Cannot determine the requested GB radius for this atom.
Writing the unmodified Bondi GB radius.
WARNING: Unbonded Hydrogen atom H22 in cnt.
Cannot determine the requested GB radius for this atom.
Writing the unmodified Bondi GB radius.
WARNING: Unbonded Hydrogen atom H23 in cnt.
Cannot determine the requested GB radius for this atom.
Writing the unmodified Bondi GB radius.
WARNING: Unbonded Hydrogen atom H24 in cnt.
Cannot determine the requested GB radius for this atom.
Writing the unmodified Bondi GB radius.
But I have got a prmtop and inpcrd file. So, can I proceed with these
files or do I have to check something?
Sanjib
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Received on Mon Feb 11 2013 - 00:00:02 PST
