On Mon, Feb 11, 2013 at 2:39 AM, Sanjib Paul <sanjib88paul.gmail.com> wrote:
> 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?
>
These warnings look worrying. I would suggest visualizing the structure
using VMD to make sure that the structure looks sane.
If the structure looks OK, I would still suggest looking at the topology
file with ParmEd to make sure that all of these hydrogen atoms actually
have bonds to a heteroatom (the warning suggests that they don't).
Good luck,
Jason
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Mon Feb 11 2013 - 03:30:03 PST
