You should use both protein (for example ff99SB, describing protein
and MG) and gaff (describing ligand) force fields simultaneously:
tleap -s -f leaprc.ff99SB
> source leaprc.gaff
> loadamberparams ligand.frcmod
> loadoff ligand.lib
> mol = loadpdb protein.pdb
> saveamberparm mol protein.prmtop protein.inpcrd
On Tue, Oct 19, 2010 at 6:12 PM, Andrew Voronkov <drugdesign.yandex.ru> wrote:
> Dear Amber users,
> I have a biotarget which has magnesium ion together with the small molecule in the binding site. I have made parametrization in GAFF with antechamber for the ligand, but then I've gota problem with magnesium ion. I actually was sure that it is included in the Amber force fields as Na+ ions and I can't find much information in manuals about this. Should I include magnesium ion in the protein or in small ligand or make a separate library for it? Should I use gaff or protein force field?
>
>> saveamberparm rab 1z2ang_w.prmtop 1z2ang_w.inpcrd
> Checking Unit.
> FATAL: Atom .R<MG 172>.A<MG 1> does not have a type.
> Failed to generate parameters
> Parameter file was not saved.
>
> Sincerely yours,
> Andrew
>
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>
--
Dmitry Nilov,
Lomonosov Moscow State University
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Received on Wed Oct 20 2010 - 07:00:04 PDT
