Hi,
I have took the minimized structure with Hydrogens added but still its
giving the same error.
QMMM: ERROR!
QMMM: Unable to achieve self consistency to the tolerances specified
QMMM: No convergence in SCF after 1000 steps.
QMMM: E = -0.1243E+07 DeltaE = 0.1060E-09 DeltaP = 0.3308E-13
QMMM: Smallest DeltaE = -0.4718E-10 DeltaP = 0.2742E-07 Step = 14
Any suggestions?
On Wed, Jun 27, 2012 at 10:20 AM, Asma Abro 28-FBAS/MSBI/F09 <
asma.msbi28.iiu.edu.pk> wrote:
> 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 10:19 AM, Asma Abro 28-FBAS/MSBI/F09 <
> asma.msbi28.iiu.edu.pk> wrote:
>
>> 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
>>>
>>>
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>
>>
>>
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Jun 27 2012 - 00:00:03 PDT
