Re: [AMBER] Fwd: SQM Error

From: Mitul Srivastava <mitul.thsti.res.in>
Date: Wed, 22 Feb 2017 13:58:48 +0530

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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> >
> >
>
>
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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 - 00:30:06 PST
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