Re: [AMBER] Fwd: SQM Error

From: Mitul Srivastava <mitul.thsti.res.in>
Date: Wed, 22 Feb 2017 13:30:22 +0530

Hello Ross,
                 Many thanks for your suggestion. I have tried this also
and have created new file without "+" sign, which is in attachment even
though it's not running.

Please find in attachments.

On Wed, Feb 22, 2017 at 1:27 PM, Bill Ross <ross.cgl.ucsf.edu> wrote:

> Do I have to spell it out :-)
>
> $ sed 's/+/ /g' lig_new.pdb > lig_new_according_to_bill.pdb
>
> Try the latter.
>
> Bill
>
>
> On 2/21/17 11:52 PM, Mitul Srivastava 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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> >
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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 - 00:30:02 PST
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