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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- application/octet-stream attachment: gdp.pdb
Received on Sun Oct 17 2010 - 11:00:04 PDT
