Hi Asma,
Perhaps there is an easier or more straightforward way of accomplishing this, but the following protocol was just sort of autopilot for me from building drug molecule structures before:
First, as your molecule consisted of only one residue, I had to open the PDB file in the vi editor and make sure all the atoms in that residue had unique names. All of your carbons had the name "C", so I renamed them C1, C2, C3, etc. As there were two hydrogens, both named "H", I renamed them H1, H2. You get the idea. If your molecule had consisted of more than one residue, you could have a C1 in each, but there just can never be two atoms with the same name in the same residue in order to load it into leap.
I wanted to make manual edits to your structure, so I loaded it into xleap, not tleap. If you just want to write another PDB file back out, you don't have to load in any force field files or anything. Just run xleap, and then load your PDB file with unique atom names into it:
x = loadpdb ligand.pdb
edit x
The edit command will bring up a GUI window where you can do some point-and-click editing. Make sure you don't have numberlock on, because this often interferes with using the GUI.
First I had to rebond all your atoms -- I did this by looking at your structure in VMD to compare and drawing all the bonds between atoms back in using xleap's "Draw" tool found in the Manipulation section along the top of the window. There is maybe an easier way to do this step, but I was used to "drawing" drug molecules almost entirely from scratch, so this was just the approach I used. Once all the bonds are reestablished, there is an option under the "Unit" menu to add hydrogens. That will fill up any remaining open valence positions with hydrogens, so you have to make sure you draw in all the other bonds you want first. If you also want to relax the structure, you can go back to the "Select" option under Manipulation, highlight your molecule, and then choose "Relax selection" from the "Edit" menu. This just cleans up the geometry a bit. Then go back to the first xleap window where you entered your text commands and save a new PDB file:
savepdb x ligand_H.pdb
quit
There you go! That's all I did to generate the structure I sent you.
Jodi
On Jun 28, 2012, at 12:57 AM, Asma Abro 28-FBAS/MSBI/F09 wrote:
> Hi Jodi,
>
> I viewed both files in VMD, hell of difference in N neighbour...you did a
> marvellous job, I am so much thankful to you. The structure is all perfect
> now, no close contacts, no overlaps...I am really thankful, can you please
> give some hint how do we add Hydrogens in xleap? and how the structure is
> relaxed?
>
> Best Regards
> Asma
>
> On Wed, Jun 27, 2012 at 8:32 PM, Jodi Ann Hadden <jodih.uga.edu> wrote:
>
>> 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
>>>>>>
>>>>>>
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>>>>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>>>>
>>>>>
>>>>>
>>>>
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Received on Thu Jun 28 2012 - 07:30:03 PDT
