Your lig_h.pdb file, which assumably contains the ligand with hydrogens added is still missing lots of hydrogens. If this is the file you're currently using, that could explain why you get the same error from sqm.
Lots of software can add hydrogens based on filling open valence bond positions, though whatever you did with chimera seems to have failed here. I loaded your original ligand.pdb into xleap and had it add hydrogens and relax the molecule, similar to what you were trying to do in chimera. Find it attached. Just be sure to visually inspect the structure this time to ensure it looks like you expect and makes sense chemically before proceeding any further.
Jodi
On Jun 27, 2012, at 2:45 AM, Asma Abro 28-FBAS/MSBI/F09 wrote:
> 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
>>>>
>>>
>>>
>>
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Received on Wed Jun 27 2012 - 09:00:02 PDT
