Re: PDB file with CONECT record

From: Prabal Maiti <>
Date: Thu 11 Apr 2002 23:27:15 -0700 (PDT)

> >... when I convert the topology and coordinate file
> > back to a pdb file using ambpdb or ptraj, I find
> > that it does not have connectivity which I
> > created/modified using xleap ... how do I get
> > back a pdb file with all new connections
> > made using xleap edit.
> ambpdb and ptraj do not translate the bonding info in
> the prmtop into pdb CONECT records. The only way to
> accomplish this is to do some programming.
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 which I have done in xleap and then saved them as
topology and coordinate file which was input for sander.
Because after I have converted my sander restart/trajectory file into pdb
file with the topology file generated with the xleap and load it back in
xleap or in cerius2/Biograph it does not have the bonds which I created
using xleap, Is there any way that I can see my structure using topology
and coordinate file without converting to pdb file.
Or any other way out,

> Bill Ross
> __________________________________________________
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Prabal K Maiti                   
Beckman Institute (139-74)             
California Institute of Technology         Tel:626-395-8151 (O)
400 South Wilson Avenue                       :626-744-1363 (H)                    
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Received on Thu Apr 11 2002 - 23:27:15 PDT
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