Hello,
I started making some dynamics for a protein which has an ATP
bound. I get the following output from leap (after reading "due
parameters" for the ATP ligand):
"
...
Building improper torsion parameters.
** 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
** Warning: No sp2 improper torsion term for CB-N*-CB-NC
atoms are: C5 N9 C4 N3
** Warning: No sp2 improper torsion term for CA-NB-CB-CB
atoms are: C6 N7 C5 C4
total 1241 improper torsions applied
...
"
The protein has 3 Trp's. I see each absent improper torsion term has as
its "center" each of the atoms that are part of both rings.
The closest to this I found at
http://structbio.vanderbilt.edu/archives/amber-archive/2009/2714.php ,
in 2009. Just to be sure, I ask if this still applies to the latest leap
version (november 2013) as I understand the other torsion terms (which
are present, eg, in parm99.dat) involving the other atoms of the ring
take care of the cited improper torsions...
Thanks,
Jorge
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Received on Fri Nov 29 2013 - 14:30:02 PST
