[gmx-users] Re: Questions

Tsjerk Wassenaar tsjerkw at gmail.com
Thu Apr 30 09:43:04 CEST 2009

Hi Lin,

> 1. Although you have explained the differece between HOH, AHOH and
> BHOH, I do not fully understand.     => Can I delete all of atoms,
> HOH, AHOH and BHOH ?

You can delete one of them, either A or B, if you want to include the
water in your model. It may be that pdb2gmx discards the B series in
favor of the A one by default, but I'm not sure about that.

> 2. So, in your tutorial, you use "united atom" algorithm, right?
> and, "pdb2gmx" can recognize the "united atoms" and give them the
> proper force fields, right?

You mix up a few things. It's the force field that is united atom (or
all atom). When running pdb2gmx you choose a force field to use to
describe your system. Based on that choice, pdb2gmx will convert your
structure in the proper way, adding all hydrogen atoms that need to be
included according to the force field.

> 3. If one want to use the "all-atom algorithm", use the command
> "protonate + protein pdb file"  first to add all missing hydrogens,
> then, use "pdb2gmx" to get an all-atom force field parameters, right?

David answered this one.

> 4. In your last email => where did you get the following information?
> => I re-check the original 1LW9.pdb => I did not get the information by myself.

It's in the file format specification, not in the file. See

> "The answer to this question is in the format specification of the PDB
> file. The A and B are alternative identifiers and indicate that the
> electron density can be explained by a water molecule that is
> partially present at two sites. If you look at the occupancy field
> you'll notice that the corresponding values are less than 1. In fact,
> if you sum the occupancies for equivalent atoms in for A and B, they
> will add up to 1."



Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623

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