AMBER Archive (2009)

Subject: Re: [AMBER] creating bond

From: Bill Ross (ross_at_cgl.ucsf.edu)
Date: Wed Jun 03 2009 - 16:40:09 CDT

> One can not create the bond in the frcmod files?

frcmod files only define params that can be used for bonds. Actual
bonds which use these parameters are defined in the topology, which
needs 'bond' cmds or graphical drawing of bonds between different
atoms. If you think about it, having all possible bonds created
between all the relevant pairs of atom types would be unchemical. That
said, it might be nice to have leap's bondbydistance command have
an option to only bond when params exist. THAT said, bondbydistance
may be what you want to use.

Bill

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