AMBER Archive (2003)

Subject: Re: protonate

From: David A. Case (case_at_scripps.edu)
Date: Mon Jun 30 2003 - 17:44:18 CDT


On Sun, Jun 29, 2003, Giulio Rastelli wrote:

> I would like to write out a PDB file with the Brookhaven naming
> convention.
> I'm using protonate -d PROTON_INFO.Brook (amber7)
>
> I noticed that the hydrogens are not aligned with the heavy atoms, and

Can you provide an example? Protonate just copies heavy atoms from the input
file, so if you input file is wrong, you output file will be the same.
In the next release, protonate will "fix" heavy atom names to the Brookhaven
format as well.

> Also, four-name hydrogens are not named
> correctly (at least not as in the PROTON_INFO.Brook file).

The proton names should match PDB (RCSB) conventions. Please provide a
specific example if you find something that is not correct. Note that the
names you see in the PROTON_INFO.Brook file do *not* look the way they
are supposed to on output.

Of course, there could be errors in the code, but we need more details.

.thanks...dave case

-- 

================================================================== David A. Case | e-mail: case_at_scripps.edu Dept. of Molecular Biology, TPC15 | fax: +1-858-784-8896 The Scripps Research Institute | phone: +1-858-784-9768 10550 N. Torrey Pines Rd. | home page: La Jolla CA 92037 USA | http://www.scripps.edu/case ==================================================================