I am using ACPYPE with ANTECHAMBER to prepare the topology using GAFF for a particular ligand. I have used it before to prepare topologies for ligands in which the charge was taken care of by adding hydrogen atoms.
However for the present ligand I have an odd number of electrons and it is creating a lot of problems. Kindly suggest how I can resolve this issue.
This is the error message :
Running: /home/user/Desktop/amber/amber14/bin/atomtype -i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff
Total number of electrons: 1767; net charge: 0
INFO: Number of electrons is odd: 1767
Please check the total charge (-nc flag) and spin multiplicity (-m flag)
Either:
- the script that adds hydrogen atoms fails in proper addition, due to strange/unusual geometry of the ligand, or
- the ligand has a net charge (is not neutral) and you should specify it when running antechamber
In the first case, inspect the ligand after adding hydrogen atoms and see it they were added in a correct way. Otherwise, check if the ligand should is neutral - if not, specify the total net charge.
Intentionally or unintentionally the ligand carries the extra hydrogen may be due to its protonation state. If it is intentionally extra hydrogens are added that means the ligand doesnt have neutral charge or charge 0, so that the following steps you can follows.
1) open the molecule in chimera.
2)tools>add charge> select force field> from there you can notified what is the exact charge on your ligand.
3) on antechamber you can type the syntax like this:
antechamber -i ligand.pdb -fi pdb -nc (required charge) -o ligand.mol2 -fo mol2 -c bcc -s 2
cheers.
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