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 - 00:00:06 PST
