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
>>>>>>>>
>>>>>>>>
>>>>>>>>
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>>>>>
>>>>> --
>>>>>
>>>>>
>>>>> *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 - 01:00:03 PST
