Try to rename MGA into MG2
2010/10/20 Andrew Voronkov <drugdesign.yandex.ru>:
> If I just load 99SB and GAFF and then .frcmod and .lib files for the small molecule then when I am trying to save .prmtop and .inpcrd files I get the next error>
>> saveamberparm rab rab.prmtop rab.inpcrd
> Checking Unit.
> FATAL: Atom .R<MGA 172>.A<MG 1> does not have a type.
> Failed to generate parameters
> Parameter file was not saved.
>>
>
> so I am curious if I should make .frcmod file and .lib files for magnesium ion or not.
> If I should that which non/bonded parameters I should use? (below is .frcmod file which I've used for zinc)
>
>
> Zinc 2+ Params
> MASS
> ZN 65.38
>
> BOND
>
> ANGL
>
> DIHE
>
> NONB
> ZN 1.85 0.06
>
>
> 20.10.10, 17:36, "Dmitry Nilov" <nilovdm.gmail.com>:
>
>> 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 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.A does not have a type.
>> > Failed to generate parameters
>> > Parameter file was not saved.
>> >
>> > Sincerely yours,
>> > Andrew
>> >
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>> > AMBER.ambermd.org
>> > http://lists.ambermd.org/mailman/listinfo/amber
>> >
>>
>>
>>
>>
>
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--
Dmitry Nilov,
Lomonosov Moscow State University
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Received on Wed Oct 20 2010 - 10:30:07 PDT
