After some modification in parameter file still I am getting the following error
ERROR: The unperturbed charge of the unit: -0.281800 is not integral.
WARNING: The unperturbed charge of the unit: -0.281800 is not zero.
-- ignoring the error and warning.
Building topology.
Building atom parameters.
For atom: .R<IAS 231>.A<H 2> Could not find vdW (or other) parameters
for type: h
For atom: .R<IAS 231>.A<OD1 11> Could not find vdW (or other)
parameters for type: o2
Parameter file was not saved.
Total unperturbed charge: -0.281800
Total perturbed charge: -0.281800
Writing pdb file: hpimt_leap.pdb
Converting N-terminal residue name to PDB format: NALA -> ALA
Converting C-terminal residue name to PDB format: CLYS -> LYS
Converting N-terminal residue name to PDB format: NVAL -> VAL
Converting C-terminal residue name to PDB format: CALA -> ALA
Quit
On Mon, Feb 22, 2016 at 4:10 PM, Bill Ross <ross.cgl.ucsf.edu> wrote:
> These are the critical lines.
>
> On 2/22/16 2:15 AM, Jesmita Dhar wrote:
>> For atom: .R<IAS 231>.A<H 2> Could not find vdW (or other) parameters
>> for type: h
>> For atom: .R<IAS 231>.A<OD1 12> Could not find vdW (or other)
>> parameters for type: o2
> It appears you are missing vdw (or other) parameters, aside from a close
> contact in your coordinate file and a nonintegral charge. For the
> missing parameters, you could investigate gaff force field files that
> might be loaded.
>
> Bill
>
>
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Received on Mon Feb 22 2016 - 03:30:04 PST
