Hello
Bonds were set in xleap (ambertools 1.5), between newly created
residues, with command:
bond unitname.residuenumber1.atomnameX unitname.residuenumber2.atomnameY
"check unitname" after each "bond" command revealed some contac
between certain atoms. Bond/angle parameters and unit OK. The log file
(verbosity 2) does not reveal anomalies. All involved residues are in
the same unit.
When the obtained top/crd file are loaded to VMD, the bonds, set as
above indicated, are not seen, i.e., the two indicated atoms are not
connected by a line.
What should I further check to check whether the bonds were established or not?
thanks
francesco pietra
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Received on Thu Mar 08 2012 - 00:00:03 PST
