[Dock-fans] How to get the charged mol for the ligand

[Devleena Shivakumar]

Hi Thomas,

Did you check the total charge? Is it 1? Does your ligand have all the
hydrogens?

Devleena

On Wed, 30 Jan 2008, Thomas Leonard wrote:


I could not get the charges for my molecule (ligand in x-crystal
structure). how to do that?
  I am getting the following error message.
  I am using chimera to do these funtions.

  Running ANTECHAMBER command: C:\Program
Files\Chimera\bin\antechamber\exe\antechamber -i
c:\docume~1\thomas\locals~1\temp\tmpkzw4il\ante.in.mol2 -fi mol2
-o c:\docume~1\thomas\locals~1\temp\tmpkzw4il\ante.out.mol2 -fo mol2 -c
bcc -nc 1 -j 5 -s 2
(IMZ)
(IMZ) Running: "C:\Program Files\Chimera\bin\antechamber"\exe\bondtype -i
ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac -j part
(IMZ)
(IMZ) Running: "C:\Program Files\Chimera\bin\antechamber"\exe\atomtype -i
ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff
(IMZ) Total number of electrons: 351; net charge: 1
(IMZ) INFO: Number of electrons is odd: 351
(IMZ)       Please check the total charge (-nc flag) and spin multiplicity
(-m flag)
Failure running ANTECHAMBER for residue IMZ


  Thomas