I think the hydrogen atoms are creating the problem. Probably tleap unable
to recognize it.
So you can remove the hydrogen atoms from your PDB file and then redo the
tleap part. tleap is quite efficient in adding hydrogen in a proper way.
Hope this help.
On Tue, Feb 2, 2016 at 2:54 PM, Sivanandam M <sivanandamphy.gmail.com>
wrote:
> Dear AMBER users,
> I have prepared topology and
> coordinates files for one protein-ligand complex using AMBERTOOLS14.
> The terminal gives the following error. please advice me to rectify
> this problem.
>
> Error
>
> WARNING: The unperturbed charge of the unit: -9.000000 is not zero.
> FATAL: Atom .R<GLU 202>.A<HE2 16> does not have a type.
> FATAL: Atom .R<HIE 253>.A<HD1 18> does not have a type.
> FATAL: Atom .R<HIE 284>.A<HD1 18> does not have a type.
> FATAL: Atom .R<GLU 285>.A<HE2 16> does not have a type.
> FATAL: Atom .R<HIE 322>.A<HD1 18> does not have a type.
> FATAL: Atom .R<HIE 387>.A<HD1 18> does not have a type.
> FATAL: Atom .R<ASP 400>.A<HD2 13> does not have a type.
> FATAL: Atom .R<HIE 405>.A<HD1 18> does not have a type.
> FATAL: Atom .R<HIE 447>.A<HD1 18> does not have a type.
> FATAL: Atom .R<ASP 494>.A<HD2 13> does not have a type.
> FATAL: Atom .R<CALA 542>.A<HXT 12> does not have a type.
> Failed to generate parameters
> Parameter file was not saved.
>
> --
>
> --------------------------------------------------------
> M.SIVANANDAM
> Research Scholar
> Department of Physics
> School of Physical Sciences
> Periyar University
> Salem-636 011
> Mobile- 9965582730, 9042066076
> --------------------------------------------------------
>
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>
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Received on Tue Feb 02 2016 - 02:00:03 PST
