AMBER Archive (2000)

Subject: bond order

From: Eoin Galligan (paxeg_at_unix.ccc.nottingham.ac.uk)
Date: Thu Jun 15 2000 - 08:32:28 CDT


Dear All,

I am trying to change bonds to double bonds within xleap. My molecule is
only a small ligand, methotrexate, and hence there are no residues.
Therefore, to change the bond order i entered

bond mtx.O mtx.C [=]

The error message i get is

bond:argument 1 is type string must be of type:[atom]

I had previously set the hybridisation of the O and C to sp2.

Obviously, I am not defining the variable of the atom correctly. How is
this done?

Any advice gratefully received.

With Regards, Eoin Galligan

tel: 0115 9515151 ext 66272
mobile: 07968 349629
mobile email: eoingalligan_at_sms.genie.co.uk

Laboratory of Biophysics and Surface Analysis,
Institute of Pharmaceutical Sciences,
Nottingham University,
University Park,
Nottingham,
NG7 2RD,
UK