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Date: Sun, 18 Feb 2007 00:54:02 -0800 (PST)
From: Francesco Pietra <chiendarret@yahoo.com>
Subject: [NWCHEM] pdb standard files
To: users nwchem <nwchem-users@emsl.pnl.gov>
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In trying to build input files for either MD of QM-MD
(NWChem 5.0) I am gertting quite confused about the
format required for pdb files that describe the
objects I want to study.

I am referring to et10.pdb (section 34.1 of manual)
and Vorpagel's edited pdb for nwchem, as found at FAQs
online section QM/MD.

The rules I know about pdb date to 1996 Is any
subsequent major change? If not, the ATOM record lacks
HET. More importantly, CONECT lacks completely. I
understand that NWChem has renounced to connectivities
even for heterogens, therefore even the MASTER record
is not present.

1st Question: is any protocol available how to
rearrange true pdb file (as I obtain them from my
pre-tools) to build input for NWChem? Must add that
coordinates from my pre-tools work perfectly for the
scf and dft modules of NWChem.

2nd Question: forgetting about CONECT does not create
problems with special bonding situations with
heterogens, especially for hydrogens?

In particular, I believe I need a description as to
the Vorpagel's table mentioned above is constructed in
order to prepare an input.

Unless I am in the far past with the pdb rules and
should be redirected to new one where CONECT and
MASTER have been abandoned.

Thanks
francesco pietra


 
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