On Thu, Feb 13, 2014 at 12:18 PM, Nitin Sharma <sharmanitin.nus.edu.sg>wrote:
> Dear amber users,
>
> while running leaprc script something caught my eye
>
> The ligand.prmtop, ligand.inpcrd and ligand.lib files were successfully
> created.
>
> # After receptor file was read, i got a warning
>
> > saveamberparm receptor receptor.prmtop receptor.inpcrd
> Checking Unit.
> WARNING: The unperturbed charge of the unit: 2.000000 is not zero.
>
> -- ignoring the warning.
>
> # However i got couple of more warnings before creating receptor.prmtop
> and receptor.inpcrd
>
> ** Warning: No sp2 improper torsion term for C*-CN-CB-CA
> atoms are: CG CE2 CD2 CE3
> ** Warning: No sp2 improper torsion term for NA-CA-CN-CB
> atoms are: NE1 CZ2 CE2 CD2
> ** Warning: No sp2 improper torsion term for C*-CN-CB-CA
> atoms are: CG CE2 CD2 CE3
> ** Warning: No sp2 improper torsion term for NA-CA-CN-CB
> atoms are: NE1 CZ2 CE2 CD2
> ** Warning: No sp2 improper torsion term for C*-CN-CB-CA
> atoms are: CG CE2 CD2 CE3
> ** Warning: No sp2 improper torsion term for NA-CA-CN-CB
> atoms are: NE1 CZ2 CE2 CD2
>
> and later receptor.pdb, receptor.lib files were also created
>
> #after this the leaprc script has to create a complex file
>
> > comp = combine {receptor UNK}
> Sequence: default_name
> Sequence: UNK
> > saveamberparm comp complex.prmtop complex.inpcrd
> Checking Unit.
> WARNING: The unperturbed charge of the unit: 1.999800 is not zero.
>
> -- ignoring the warning.
>
> Building topology.
> Building atom parameters.
> Building bond parameters.
> Building angle parameters.
> Building proper torsion parameters.
> Building improper torsion parameters.
>
> # I got similar warning again
>
> ** Warning: No sp2 improper torsion term for NA-CA-CN-CB
> atoms are: NE1 CZ2 CE2 CD2
> ** Warning: No sp2 improper torsion term for C*-CN-CB-CA
> atoms are: CG CE2 CD2 CE3
> ** Warning: No sp2 improper torsion term for NA-CA-CN-CB
> atoms are: NE1 CZ2 CE2 CD2
> ** Warning: No sp2 improper torsion term for C*-CN-CB-CA
> atoms are: CG CE2 CD2 CE3
> ** Warning: No sp2 improper torsion term for NA-CA-CN-CB
> atoms are: NE1 CZ2 CE2 CD2
> ** Warning: No sp2 improper torsion term for C*-CN-CB-CA
> atoms are: CG CE2 CD2 CE3
>
> NOW MY QUESTION IS:
>
> 1) what is cause of the warning related to improper torsion terms "**
> Warning: No sp2 improper torsion term for NA-CA-CN-CB" and can i ignore
> the warning
>
>
The warning is to inform you that there are no improper terms between those
atoms. Impropers are typically added to keep a set of 4 atoms planar (like
in conjugated ring systems, for instance). They are not always necessary,
so this warning can be safely ignored.
>
>
>
>
>
> 2) while creating receptor.prmtop receptor.inpcrd the unperturbed charge
> of the unit: 2.000000 the how it was reduced to 1.999800 while creating
> complex.prmtop complex.inpcrd ?
>
Your ligand must have a charge of -0.0002. This is not at all unusual for
systems whose charges are derived using antechamber (and such a tiny charge
deviation is not cause for concern).
>
> 3) to neutralize the system i added 2 Cl- ions by command
> however, after that Total unperturbed charge was -0.000200
> So will this little charge of -0.000200 have any influence on MD
> simulation? if yes, how can i make the system completely neutral?
>
I do not think you could possibly notice the effect of -0.0002 electron
charges in your system. You could make the system completely neutral by
editing the ligand library file (mol2 or amber prep) and add a charge of
0.0002 to one of the atoms there.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Thu Feb 13 2014 - 10:30:03 PST
