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
>>
>>
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>>
>
>
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Received on Tue Jun 26 2012 - 22:30:06 PDT
