Why don't you check the topology with rdparm (and its "bonds" command)?
Lorenzo Gontrani
2012/3/8 Francesco Pietra <chiendarret.gmail.com>:
> 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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--
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Lorenzo Gontrani
Research associate of EDXD group
University of Rome "La Sapienza"
GSM +39 338 7615798
Email l DOT gontrani AT caspur DOT it
Webpage: http://webcaminiti/gontrani.html
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Received on Thu Mar 08 2012 - 01:00:03 PST
