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
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Feb 26 2016 - 10:00:04 PST
