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
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>>
>>
>> ---------- 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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Received on Wed Feb 22 2017 - 00:00:04 PST
