On Sat, Apr 19, 2014 at 6:22 AM, 石坪江梨花 <13lb010p.rikkyo.ac.jp> wrote:
> Dear all,
>
> I have tried HOH for the residue name for water,
>
>
> HETATM1 O HOH 1 -5.382 16.838 -57.659 1.00 0.00
> O
> HETATM2 H1 HOH 1 -4.602 17.179 -58.121 1.00 0.00 H
> HETATM3 H2 HOH 1 -5.047 16.021 -57.260 1.00 0.00 H
>
Where did you get this PDB? The columns are completely wrong, and no PDB
parser should be expected to correctly parse this file (although some might
by accident). Whatever method you used to generate this PDB file, don't
use it again.
END
>
>
> but there was the following error .
>
> -- residue 1: duplicate [ HO] atoms (total 3)
> Warning: Atom names in each residue should be unique.
> (Same-name atoms are handled by using the first
> occurrence and by ignoring the rest.
> Frequently duplicate atom names stem from alternate
> conformations in the PDB file.)
>
This tells you that tleap is interpreting the atom names as " HO", which
is the 2 spaces before and the first 2 letters of the "HOH" residue name.
This is clearly not what you intended with your file.
Unknown residue: number: 0 type: Terminal/last
>
This tells you that tleap is creating a blank residue, since the residue
name (which should be HOH) could not be found in the PDB file. It also
tells you that the residue number is not being found correctly.
> ..relaxing end constraints to try for a dbase match
> -no luck
> Creating new UNIT for residue: sequence: 1
Created a new atom named: HO within residue: .R< 1>
> total atoms in file: 3
> The file contained 1 atoms not in residue templates
>
Here you see that tleap has thrown out the second two atoms of your file.
It does this because it thinks each atom is named HO, and it only keeps
the first occurrence of each atom (as it promised to do above).
I'm really not sure what the problem is.
>
You have at least one problem, probably two.
First, you need a correctly-formatted PDB file. You can download the PDB
format specification and fix your file above by hand, or you can use
another tool to build your system, like Avogadro, ghemical, xleap, etc.,
and use that tool to write out a correct PDB file.
Second, you have to make sure that you load a residue library (and a
corresponding parameter file) for the water residue. The easiest way to do
that is to simply load one of the standard protein force fields, like
leaprc.ff12SB or leaprc.ff14SB (with AmberTools 14). There's no reason to
use gaff if all you are parametrizing is a single water molecule.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Sat Apr 19 2014 - 05:00:02 PDT
