Re: [AMBER] Fwd: SQM Error

From: Mitul Srivastava <mitul.thsti.res.in>
Date: Wed, 22 Feb 2017 13:22:04 +0530

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




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Received on Wed Feb 22 2017 - 00:00:05 PST
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