AMBER Archive (2009)

Subject: Re: [AMBER] non standard residue and bond command

From: case (case_at_biomaps.rutgers.edu)
Date: Wed Dec 16 2009 - 15:06:34 CST

On Wed, Dec 16, 2009, Neha Bharat Gajaria wrote:
>
> I have a big molecule which I cannot run directly using antechamber.
> So I split the residues into 4 parts HE1, HE2, HE3 and HE4
> respectively and convert them to prepi files as well as change the
> residue name accordingly in PDB file. I used TER between each residue
> in pdb file to avoid the warnings for long distance between two atoms
> as per suggestions in amber archives.

I don't understand why you have long distances between atoms...is that true
for the coordinates you are inputting? Check these distances by hand. Are
they wrong in the pdb file?

>
> I load the prepi files first, then the pdb file. I try to use bond
> command and try to connect with single bond between two residues e.g.
> HE1.O60 and HE2.C39 Now as the residues are from two different units,
> the bond command doesnt create a single bond, there are no errors or
> warnings but I simply dont see a bond between two residues when I try
> to save a new pdb file.

When you say you "don't see a bond" what do you mean? Are you using xleap
or some other visualization program? Connectivities are not in the pdb files,
so visualization programs have to guess. If you indeed have the "long
distances" mentioned above, a pdb visualization program might decide there
is no bond.

You can use the "desc" command in LEaP to see what bonds are actually in your
system.

....dac

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