"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
> >>
> >> _______________________________________________
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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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> > http://lists.ambermd.org/mailman/listinfo/amber
>
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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 - 00:30:04 PST
