AMBER Archive (2002)

Subject: Re: PDB file with CONECT record

From: Miguel Angel (riojas_miguel_at_hotmail.com)
Date: Fri Apr 12 2002 - 05:03:09 CDT

> > Ok, I understand that ambpdb and ptraj dont genertae
> > CONECT records, but then how do I see my sander
> > minimized/dynamics structure with the
> > modified/edited bond
>
> Modify ambpdb or ptraj (or carnal) to add CONECT
> records. Or perhaps MOILview can get bond info from
> prmtop - it wouldn't surprise me.
>

One easy way to do that is passing through the XmMol program. You load the
pdb file, then you add or delete connections, and when you save it (in a pdb
format) you will get all the CONNECT lines at the end of the file.
XmMol is freely distributed to licensed academic institutions.
http://condor.urbb.jussieu.fr/logiciels/XmMol.html

Miguel Angel.