[AMBER] Viewing with VMD bonds set by the "bond" command

From: Francesco Pietra <chiendarret.gmail.com>
Date: Thu, 8 Mar 2012 08:59:23 +0100


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?


francesco pietra

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Received on Thu Mar 08 2012 - 00:00:03 PST
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