AMBER Archive (2002)

Subject: Re: PDB file with CONECT record (fwd)

From: David Case (case_at_scripps.edu)
Date: Tue Apr 09 2002 - 22:30:38 CDT

On Tue, Apr 09, 2002, Prabal Maiti wrote:

> 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.

LEaP may read these records, but I don't think it does anything with
them. The requirement is that leap recognized each residue in your pdb
file, and match it up with the corresponding residue in its library.
It then tries to match up the atoms in the input pdb file with the
ones in the library. If there are missing atoms in the input file, it
will build them. If there are "extra" atoms in the input file (not
recognized by LEAP), it will warn you, and will almost never do the right
thing with these atoms. Basically, you *must* ensure that every residue
in your input pdb file is correclty recognized, and that the atoms match
up with what leap expects. Once that happens, the atoms are bonded
according to what is in the residue file, plus any addtional bonds you
may choose to add with the "bond " command.
>
> 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.

ambpd makes no attempt to create CONECT records, not I think, does ptraj.
You can use the "rdparm" routine to write out all of the bonds to see if
things are exactly what you want.

> 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.

I think you would have to modify ambpdb to write out this information.

....hope this helps....good luck....dac 

-- 

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David A. Case                     |  e-mail:      case_at_scripps.edu
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