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>___________________
>> ____________________________
>>> 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
Received on Wed Feb 22 2017 - 00:30:05 PST
