Also, if no sqm.out, does
$ /apps/gnu/gcc-4.8.5-4/amber/16/amber16//bin/sqm
run at all?
Bill
On 2/22/17 12:27 AM, Bill Ross 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
>>>>>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>>>> _______________________________________________
>>>>>> AMBER mailing list
>>>>>> AMBER.ambermd.org
>>>>>> 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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>>
>
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Received on Wed Feb 22 2017 - 01:00:02 PST
