Never mind rotating, I was going on the assumption that you had a valid
setup to start with. Dr. Goetz's advice addresses the real point.
Bill
On 2/22/17 12:54 AM, Bill Ross wrote:
> By the way, I've never run the code in question.
>
> Does the orientation in the pdb matter? I.e. is the ligand positioned
> relative to the protein?
>
> It's another shot in the dark, but what if you rotated the ligand or (if
> positioning is relative) the whole complex?
>
> Bill
>
>
> On 2/22/17 12:45 AM, Mitul Srivastava wrote:
>> Dear Ross,
>> There are no close contacts. And I have successfully
>> completed simulation using this ligand on three complexes. The protein is
>> same, ligand is same, but on others it has worked properly but only in this
>> case it's showing this error and I am surprised why it's happening. I have
>> no clue what to do.
>>
>> On Wed, Feb 22, 2017 at 2:10 PM, Bill Ross <ross.cgl.ucsf.edu> wrote:
>>
>>> It looks like SQM simply doesn't like those coordinates. Are you sure
>>> there aren't any close contacts?
>>>
>>> Bill
>>>
>>>
>>> On 2/22/17 12:28 AM, Mitul Srivastava wrote:
>>>> yes it is, this is the error coming, you can also find in attached.
>>>>
>>>> QMMM: ERROR!
>>>> QMMM: Unable to achieve self-consistency to the tolerances specified
>>>>
>>>> On Wed, Feb 22, 2017 at 1:57 PM, Bill Ross <ross.cgl.ucsf.edu> wrote:
>>>>
>>>>> Is there an sqm.out file left behind? If so, how does it end?
>>>>>
>>>>> Bill
>>>>>
>>>>>
>>>>> On 2/22/17 12:24 AM, Mitul Srivastava wrote:
>>>>>> "Error: cannot run "/apps/gnu/gcc-4.8.5-4/amber/16/amber16//bin/sqm -O
>>>>> -i
>>>>>> sqm.in -o sqm.out" of bcc() in charge.c properly, exit"
>>>>>>
>>>>>> this is the error.
>>>>>>
>>>>>> And I have not added hydrogens before running antechamber.
>>>>>>
>>>>>> On Wed, Feb 22, 2017 at 1:39 PM, Goetz, Andreas <agoetz.sdsc.edu>
>>> wrote:
>>>>>>> You still haven’t told what is the error that you encounter with
>>>>>>> lig_new.pdb. And did you add hydrogen atoms before running
>>> antechamber?
>>>>>>> As a note aside, if you have twice the same ligand, you have to run
>>>>>>> antechamber only once.
>>>>>>>
>>>>>>> All the best,
>>>>>>> Andy
>>>>>>>
>>>>>>> —
>>>>>>> Dr. Andreas W. Goetz
>>>>>>> Assistant Project Scientist
>>>>>>> San Diego Supercomputer Center
>>>>>>> Tel: +1-858-822-4771
>>>>>>> Email: agoetz.sdsc.edu
>>>>>>> Web: www.awgoetz.de
>>>>>>>
>>>>>>>> On Feb 21, 2017, at 11:52 PM, Mitul Srivastava <mitul.thsti.res.in>
>>>>>>> wrote:
>>>>>>>> Sir,
>>>>>>>> I have two complexes with same ligand only there docking
>>>>> position
>>>>>>>> is different. When I am running antechamber with 1st attached file
>>> from
>>>>>>>> where i have extracted the ligand and saved it as "lig.pdb", its
>>>>> running
>>>>>>>> properly generating every file. But when I am running antechamber for
>>>>>>>> second attached file, its not running. Though my deepest query is
>>> that
>>>>>>> both
>>>>>>>> the ligands are same only there is difference in coordinates even
>>>>> though
>>>>>>>> second is not running.
>>>>>>>>
>>>>>>>> I think I am clear this time.
>>>>>>>>
>>>>>>>> Please help me
>>>>>>>>
>>>>>>>> On Wed, Feb 22, 2017 at 1:12 PM, Goetz, Andreas <agoetz.sdsc.edu>
>>>>> wrote:
>>>>>>>>> What do you mean with “running fine” and “sqm error”? Without
>>> details
>>>>>>> it’s
>>>>>>>>> hard to help. The pdb files don’t have hydrogen atoms, did you add
>>>>> these
>>>>>>>>> before running antechamber?
>>>>>>>>>
>>>>>>>>> All the best,
>>>>>>>>> Andy
>>>>>>>>>
>>>>>>>>> —
>>>>>>>>> Dr. Andreas W. Goetz
>>>>>>>>> Assistant Project Scientist
>>>>>>>>> San Diego Supercomputer Center
>>>>>>>>> Tel: +1-858-822-4771
>>>>>>>>> Email: agoetz.sdsc.edu
>>>>>>>>> Web: www.awgoetz.de
>>>>>>>>>
>>>>>>>>>> On Feb 21, 2017, at 11:28 PM, Bill Ross <ross.cgl.ucsf.edu> wrote:
>>>>>>>>>>
>>>>>>>>>> Not sure what the SQM error is, but looking at the pdb's, I notice
>>>>> the
>>>>>>>>>> 2nd has explicit '+'s in it, which might confuse some programs.
>>>>>>>>>>
>>>>>>>>>> Bill
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> On 2/21/17 10:53 PM, Mitul Srivastava wrote:
>>>>>>>>>>> ---------- Forwarded message ----------
>>>>>>>>>>> From: <amber-owner.ambermd.org>
>>>>>>>>>>> Date: Wed, Feb 22, 2017 at 12:03 PM
>>>>>>>>>>> Subject: SQM Error
>>>>>>>>>>> To: mitul.thsti.res.in
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> You are not allowed to post to this mailing list, and your message
>>>>> has
>>>>>>>>>>> been automatically rejected. If you think that your messages are
>>>>>>>>>>> being rejected in error, contact the mailing list owner at
>>>>>>>>>>> amber-owner.ambermd.org.
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> ---------- Forwarded message ----------
>>>>>>>>>>> From: Mitul Srivastava <mitul.thsti.res.in>
>>>>>>>>>>> To: amber.ambermd.org
>>>>>>>>>>> Cc:
>>>>>>>>>>> Date: Wed, 22 Feb 2017 12:03:04 +0530
>>>>>>>>>>> Subject: SQM Error
>>>>>>>>>>> Hello Amber Users,
>>>>>>>>>>> i am doing protein-ligand complex
>>> study
>>>>>>>>> and I
>>>>>>>>>>> am facing a very unique error where the error is showing while
>>>>> running
>>>>>>>>>>> ANTECHAMBER on Amber16. The error is -- I have used two proteins
>>>>> with
>>>>>>>>> same
>>>>>>>>>>> ligand. In attached file "lig.pdb" of one complex is running fine
>>>>>>> while
>>>>>>>>>>> "lig_new.pdb" is not running and is showing the sqm error. though
>>>>> both
>>>>>>>>> the
>>>>>>>>>>> ligands are same and I am surprised why this error is coming.
>>>>>>>>>>>
>>>>>>>>>>> please help me as I am not able to troubleshoot.
>>>>>>>>>>>
>>>>>>>>>>> thank you
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> _______________________________________________
>>>>>>>>>>> AMBER mailing list
>>>>>>>>>>> AMBER.ambermd.org
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>>>>>>>>>> _______________________________________________
>>>>>>>>>> AMBER mailing list
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>>>>>>>>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>>>>>>> _______________________________________________
>>>>>>>>> AMBER mailing list
>>>>>>>>> AMBER.ambermd.org
>>>>>>>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>>>>>>>
>>>>>>>> --
>>>>>>>>
>>>>>>>>
>>>>>>>> *Mitul SrivastavaSenior Research FellowD*rug *D*iscovery *R*esearch
>>>>>>> *C*enter
>>>>>>>> (DDRC)
>>>>>>>> *T*ranslational *H*ealth *S*cience and *T*echnology *I*nstitute
>>>>> (THSTI),
>>>>>>>> NCR Biotech Science Cluster
>>>>>>>> 3rd Milestone, Faridabad – Gurgaon Expressway
>>>>>>>> PO box #04, Faridabad – 121001, India
>>>>>>>> <comp_usp7_s0.pdb><comp_lowest.pdb>___________________
>>>>>>> ____________________________
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Received on Wed Feb 22 2017 - 01:30:02 PST
