I guess we will need to know what is the SQM error? Is it the same with
the new file? Is it text that you can paste here?
On 2/22/17 12:00 AM, Mitul Srivastava wrote:
> 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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Received on Wed Feb 22 2017 - 00:30:03 PST
