No, It exits immediately.
On Wed, Feb 22, 2017 at 2:00 PM, Bill Ross <ross.cgl.ucsf.edu> wrote:
> 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
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> >>>>> _______________________________________________
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> >>>>> 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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> >
>
>
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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
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Received on Wed Feb 22 2017 - 01:00:02 PST
