Dear Andrew (I'am answering to myself, but maybe this can be useful),
as you can see from this thread:
http://archive.ambermd.org/200911/0187.html
such an error might be a result from non-zero cahrge of the molecule.
If the molecule is charged in the system of interest, please use the -nc flag with antechamber as in the example below:
antechamber -i gdp3.pdb -fi pdb -nc -3 -o gdp3.mol2 -fo mol2 -c bcc -s 2
Please notice that (page 83, AmberTools 11 manual) "Also note that this procedure
depends heavily upon the initial 3D structure: it must have all hydrogens present, and the
charges computed are those for the conformation you provide, after minimization in the AM1
Hamiltonian. In fact, this means that you must have an reasonable all-atom initial model of
your molecule (so that it can be minimized with the AM1 Hamiltonian), and you may need to
specify what its net charge is, especially for those molecular formats that have no net charge
information, and no partial charges or the partial charges in the input are not correct. The
system should really be a closed-shell molecule, since all of the atom-typing rules assume this
implicitly."
Don't hesitate to ask any further questions.
Sincerely yours,
Andrew
17.10.10, 21:35, "Andrew Voronkov" <drugdesign.yandex.ru>:
> Dear Amber users,
> I am trying to make parametrization for GDP and have taken GDP file to Reduce software, have added the hydrogens and I get the error below.
> As I understand this is because the number of atoms is odd. In the PDB (code 1z2a or 1z22) there is also Mg ion in the binding site of GDP. How is better to correct the GDP sturcture and prepare it for antechamber in this case? Should I include magnesium ion as part of ligand file (if it is complexed by phosphate group) or include it with rest of the protein for parametrization in such a case and how to neutralize phosphate group then if this causes the problem with antechamber? How can I modify this file (attached) so that there will be normal number of electrons?
>
>
>
> [voronkov.t60-2 Rab23]$ antechamber -i gdp2.pdb -fi pdb -o gdp2.mol2 -fo mol2 -c bcc -s 2
> Running: /home/osolodkin/amber10/bin/bondtype -j full -i ANTECHAMBER_BOND_TYPE.A C0 -o ANTECHAMBER_BOND_TYPE.AC -f ac
>
>
>
> Running: /home/osolodkin/amber10/bin/atomtype -i ANTECHAMBER_AC.AC0 -o ANTECHAMB ER_AC.AC -p gaff
>
> Total number of electrons: 225; net charge: 0
> INFO: Number of electrons is odd: 225
> Please check the total charge (-nc flag) and spin multiplicity (-m flag)
>
> Running: /home/osolodkin/amber10/bin/mopac.sh
> Error: unable to find mopac charges in mopac.out
>
>
>
> What can be the problem?
>
> Sincerely yours,
> Andrew
>
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Received on Tue Oct 19 2010 - 05:30:04 PDT
