AMBER Archive (2002)

Subject: Re: PDB file with CONECT record

From: Prabal Maiti (maiti_at_wag.caltech.edu)
Date: Fri Apr 12 2002 - 01:27:15 CDT

> >... 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,
Prabal

> Bill Ross
>
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-- 
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Prabal K Maiti                             Email:maiti_at_wag.caltech.edu
Beckman Institute (139-74)                       pkmaiti_at_yahoo.com
California Institute of Technology         Tel:626-395-8151 (O)
400 South Wilson Avenue                       :626-744-1363 (H)                    
Pasadena, CA 91125                         Fax:626-585-0918
                                           Home add: 110 S. Michigan Ave.
http://www.wag.caltech.edu/home/maiti      Apt # 19, Pasadena, CA 91106
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