AMBER Archive (2009)
Subject: Re: [AMBER] non standart residue library creation with tleap (Zn atom)
From: FyD (fyd_at_q4md-forcefieldtools.org)
Date: Mon Nov 23 2009 - 07:25:15 CST
This frcmod file should only contains vdW parameters:
This takes 3 sec to do it by hands.
When you do all automatically, you do not understand what you do...
You just need to find these vdW parameters in the required paper:
replace xxxx yyyy by the Zinc vdW parameters...
> Hm, frcmod should be prepared by antechamber. Now we got antechamber
> error here:
> $ antechamber -i zn2.pdb -fi pdb -o zn2.prepin -fo prepi -c bcc -s 2
> Running: /amber10/bin/atomtype -i ANTECHAMBER_AC.AC0 -o
> ANTECHAMBER_AC.AC -p gaff
> Total number of electrons: 0; net charge: 0
> Running: /amber10/bin/mopac.sh
> Error: unable to find mopac charges in mopac.out
> This is zn2.pdb, maybe there is something wrong with PDB file:
> HETATM 1666 ZN ZN2 1 -34.053 -24.945 -27.759 1.00 27.33
> 20.11.09, 18:47, "FyD" <fyd_at_q4md-forcefieldtools.org>:
>> Quoting Andrew Voronkov :
>> > 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.A 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
>> > 20.11.09, 16:40, "FyD" :
>> >> 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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