> +--- Sp0 probably means a new atom type is involved
> +--- which needs to be added via addAtomTypes
You could look in the default leaprc for examples of atom type definitions. ND1 seems to be the problem, but that's an atom name I think - probably you need to map the amber atom type (not name) to the leap hybridization.
> addIons: 1st Ion & target are the same charge:
can't neutralize.
You need to neutralize with ions opposite in charge to the net of the unit.
> ERROR: The unperturbed charge of the unit: -2.552792 is not integral.
Did you calculate your own charges?
> Could not find bond parameter for: OW - ZN
You bonded Zn to water?
> Could not find angle parameter: NQ - ZN - O2
You could either use restraints to hold your Zn in place, or derive all
the missing parameters that come from bonding it to other atoms.
If you haven't looked at the tutorials yet, you may find some answers there.
Bill
On 12/13/15 10:47 PM, Xiong Jiawei wrote:
> Dear friends,
>
>
> I am a new user to Amber software and I am currently using Amber14 to run MD simulation of a zinc-containing protein.
>
>
> I tried to use the ZAFF force field obtained from the ZAFF Modelling Tutorial online and followed the steps described in the tutorial, but I've gotten problems as follows:
>
>
> Prob1
>
> Reading title:
> ZAFF parameter set created by MTK++/MCPB
> Loading PDB file: ./4jij_complex_zn_new_renamed.pdb
> +Currently only Sp3-Sp3/Sp3-Sp2/Sp2-Sp2 are supported
> +---Tried to superimpose torsions for: *-CE1-ND1-*
> +--- With Sp2 - Sp0
> +--- Sp0 probably means a new atom type is involved
> +--- which needs to be added via addAtomTypes
> +Currently only Sp3-Sp3/Sp3-Sp2/Sp2-Sp2 are supported
> +---Tried to superimpose torsions for: *-CG-ND1-*
> +--- With Sp2 - Sp0
> +--- Sp0 probably means a new atom type is involved
> +--- which needs to be added via addAtomTypes
> +Currently only Sp3-Sp3/Sp3-Sp2/Sp2-Sp2 are supported
> ......
>
> Prob2
> addIons: 1st Ion & target are the same charge:
> can't neutralize.
> ......
> ERROR: The unperturbed charge of the unit: -2.552792 is not integral.
> WARNING: The unperturbed charge of the unit: -2.552792 is not zero.
>
> Prob3
> Building topology.
> Building atom parameters.
> Building bond parameters.
> Could not find bond parameter for: OW - ZN
> Building angle parameters.
> Could not find angle parameter: NQ - ZN - O2
> Could not find angle parameter: O2 - ZN - NP
> Could not find angle parameter: O2 - ZN - E2
> Could not find angle parameter: C - O2 - ZN
> Could not find angle parameter: N5 - ZN - OW
> Could not find angle parameter: N6 - ZN - OW
> Could not find angle parameter: N7 - ZN - OW
> Could not find angle parameter: HW - OW - ZN
> Could not find angle parameter: HW - OW - ZN
>
> As for the first problem, I have tried to use "addAtomtypes" to specify the hybridization state for "ND1", "NE2" and so on. However, it seemed like my command was not recognized by the programme. This is what I wrote:
>
> addAtomTypes { { "ZN" "Zn" "sp3" } { "N2" "N" "sp3" } { "ND1" "N" "sp2" } { "NE2" "N" "sp2" } }
>
> Could anyone help me in these problems? Thanks a lot!!!
>
> Jiawei
>
>
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Received on Sun Dec 13 2015 - 23:30:04 PST
