Re: [AMBER] waters inside cavity

From: Niel Henriksen <shireham.gmail.com>
Date: Fri, 26 Feb 2016 09:59:11 -0800

Hi Elisa,

LEaP doesn't recognize the atom names for your water. Try changing them to
the following standard names:

HETATM 3620 O HOH A 221 34.044 38.871 15.205 1.00-30.75
  O
HETATM 3621 H1 HOH A 221 34.935 39.223 15.493 1.00 0.00
  H
HETATM 3622 H2 HOH A 221 33.321 39.338 15.714 1.00 0.00
  H

Best,
--Niel


On Fri, Feb 26, 2016 at 7:00 AM, Elisa Pieri <elisa.pieri90.gmail.com>
wrote:

> Hi everybody,
>
> I'm using this leap input:
>
> source leaprc.constph
> loadAmberPrep ret.prepin
> loadAmberParams frcmod2.cro
> loadAmberParams frcmod1.cro
> prot = loadPDB initial.pdb
> saveAmberParm prot prot.parm7 prot.rst7
> quit
>
> on a pdb file that contains these lines:
>
> HETATM 3620 OW HOH A 221 34.044 38.871 15.205
> 1.00-30.75 O
> HETATM 3621 HW1 HOH A 221 34.935 39.223 15.493 1.00
> 0.00 H
> HETATM 3622 HW2 HOH A 221 33.321 39.338 15.714 1.00
> 0.00 H
>
> But the result is:
>
> FATAL: Atom .R<WAT 221>.A<OW 4> does not have a type.
> FATAL: Atom .R<WAT 221>.A<HW1 5> does not have a type.
> FATAL: Atom .R<WAT 221>.A<HW2 6> does not have a type.
> Failed to generate parameters
> Parameter file was not saved.
> Quit
>
> Now..I guess that thire must be a pretty stupid mistake, but I don't know
> where. Can you help me?
> Elisa
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>
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Received on Fri Feb 26 2016 - 10:00:04 PST
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