AMBER Archive (2009)

Subject: Re: [AMBER] non standart residue library creation with tleap (Zn atom)

From: FyD (fyd_at_q4md-forcefieldtools.org)
Date: Fri Nov 20 2009 - 11:47:00 CST

Quoting Andrew Voronkov <drugdesign_at_yandex.ru>:

> Ok, interesting. The "Unknown residue" message doesn't appear
> anymore while loading pdb...but I have now problem in saving amber
> params files:
>
> Building topology.
> Building atom parameters.
> For atom: .R<ZN2 1311>.A<ZN 1> Could not find type: ZN
> Parameter file was not saved.

See updated http://q4md-forcefieldtools.org/Help/Andrew/tleap.cmd
& BTW do not forget to prepare a "frcmod" file for setting vdW
parameters for your Zinc atom, I forgot to add this step

F.

> 20.11.09, 16:40, "FyD" <fyd_at_q4md-forcefieldtools.org>:
>
>> Andrew,
>>
>> > Yes! It works now! The problem was that I've changed the atom name
>> > rather than residue name in PDB and also residue name was also
>> > shifted a bit left and was at last stage not ZN2 but N2.
>>
>> ok. This is a classical problem of recognition between your PDB & the
>> FF libraries you load in LEaP.
>>
>> > I also wonder if it's ok to setup charge Zn2+ to a metal ion bound
>> > to four amino acids or I should set up it as part of the protein then.
>>
>> Two approaches are possible:
>> - The 1st one you consider Zn2+ not physically connected to your
>> ligands & the total charge of the atom Zn is +2 (BTW do not forget to
>> prepare a "frcmod" file for setting vdW parameters for your Zinc atom,
>> I forgot to add this step @
>> http://q4md-forcefieldtools.org/Help/Andrew/tleap.cmd).
>> - The second one you derive charges for your Zn-complex were you will
>> consider connections between Zinc & well-established ligands. In this
>> case, the charge of Zn2+ should decreased to... some value ;-)
>> I suggest you to use R.E.D.-III.3 and/or R.E.D. Server/R.E.D.-IV in
>> the latter case.
>>
>> regards, Francois
>>
>>
>>
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>>
>>
>
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           F.-Y. Dupradeau
                 ---
http://q4md-forcefieldtools.org/FyD/

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