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
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 ?
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 have attached the files that I thought can help to explain the problem a bit more.
Thanks and regards,
Nitin Sharma
Department of Pharmacy,Faculty of Science,National University of Singapore,block S7, Level 2, Singapore : sharmanitin.nus.edu.sg<mailto:sharmanitin.nus.edu.sg> ; http://www.linkedin.com/in/imsharmanitin
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- application/octet-stream attachment: mopac.out
- application/octet-stream attachment: mopac.pdb
Received on Thu Feb 13 2014 - 09:30:02 PST
