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 - 22:00:03 PDT
