I am attaching the lig_h.pdb file here. When I minimize the structure with
the help of chimera, it adds missing Hydrogen atoms but still I get errors.
Yeah by adding Hydrogens, the charge is neutral. How to add Hydrogens
manually?
Thanks.
Asma
On Wed, Jun 27, 2012 at 9:42 AM, Ross Walker <ross.rosswalker.co.uk> wrote:
> Hi Asma,
>
> What does ligand_h.pdb look like? - You are missing MANY hydrogens in this
> PDB. You may need to add them yourself manually. Without the hydrogens it
> is
> no wonder the SCF does not converge. Ligand.pdb as it stands does not
> represent a stable molecule.
>
> Additionally how are you arriving at a charge of +1 for this ligand. It
> seems to me that once it has had the hydrogens added the charge would be
> neutral.
>
> All the best
> Ross
>
> > -----Original Message-----
> > From: Asma Abro 28-FBAS/MSBI/F09 [mailto:asma.msbi28.iiu.edu.pk]
> > Sent: Tuesday, June 26, 2012 8:40 PM
> > To: AMBER Mailing List
> > Subject: [AMBER] AMBER Error: unable to achieve consistency
> >
> > Hi all,
> >
> > I have a pdb structure of a ligand. (Attached with the mail)
> >
> > when I run the command
> >
> > reduce ligand.pdb > ligand_h.pdb
> >
> > It results in "found 2 Hydrogens, standardized 2 Hydrogens". It does
> > not
> > add missing Hydrogens. However I run the antechamber command:
> >
> > antechamber -i ligand.pdb -fi pdb -o dock.mol2 -fo mol2 -c bcc -nc 1
> >
> > the sqm.out file has the error:
> >
> > QMMM: ERROR!
> > QMMM: Unable to achieve self consistency to the tolerances specified
> > QMMM: No convergence in SCF after 1000 steps.
> > QMMM: E = -0.7011E+06 DeltaE = 0.1272E+00 DeltaP = 0.3207E-01
> > QMMM: Smallest DeltaE = 0.5661E-02 DeltaP = 0.3063E-01 Step =
> > 94
> >
> > can anyone help me out with this problem?
> >
> > Regards
>
>
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Received on Tue Jun 26 2012 - 22:30:06 PDT
