AMBER Archive (2002)

Subject: PDB file with CONECT record (fwd)

From: Prabal Maiti (maiti_at_wag.caltech.edu)
Date: Tue Apr 09 2002 - 20:04:50 CDT

Can someome help me with my second problem (below).
Prabal

---------- Forwarded message ----------
Date: Mon, 8 Apr 2002 12:06:21 -0700 (PDT)
From: Prabal Maiti <maiti_at_intel4.wag.caltech.edu>
To: AMBER mailing list <amber_at_heimdal.compchem.ucsf.edu>
Subject: PDB file with CONECT record

I have a pdb file for a double crossover DNA molecule (prepared by Biograf
from MSI) with connectivity record. When I load the pdb file I find that
xleap automatically
connects more at the crossover (like the P is connected to O5' at all
the crossovers going from one chain to other)). These connections are not
in the connectivity record. Since Xleap does not show the atom number I am
not able to figure out which atom number is connecting to which one.
ALso it does not keep some of its origianl connectivity record, Like I
have nicked the two chains at few locations
and have connected them with PO2 to have the crossovers, These
connectivity records are in pdb file, But when I load them in xleap it
does not show these connections. I checked the source code and it seems
leap reads the connectivity info (pdb_read.c, and pdbFile.c). Can some
one suggest how to keep the original connectivity record of the
pdb file while reading in xleap.

Second problem:
After I have loaded my pdb file in xleap, I have deleted the
extra connection xleap was generating and added few extra connectiion
where the two double chain should cross over by using the edit command in
xleap. And I save it as a unit using saveoff command. Also I save it as
.top and .crd file for my sander runs.But 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
edit. Same problem when I convert my sander restart file to pdb file. So I
am wondering when using the topology and coordinate file created by xleap
whether it has the connectivity which was created
using xleap. Also how do I get back a pdb file with all new connections
made using xleap edit.
 
Thanks for any suggestions.
Prabal 

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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)                    
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