Re: [AMBER] Antechamber trouble with COA-acyl chain

From: Erin Kelly <erkelly4572.gmail.com>
Date: Thu, 14 Jul 2011 09:07:46 -0500

Dr. Case,

I came back this morning to find that antechamber had generated the .mol2
(attached). Thank you very much for your help; we are now better equipped
to attempt this with other CoA structures. Of course we'll use better
starting geometries than the first one I sent...

Thanks,
Erin

On Wed, Jul 13, 2011 at 5:08 PM, Erin Kelly <erkelly4572.gmail.com> wrote:

> That may have been the case; I'm running it again and I'll get back to
> you.
>
> Erin
>
>
> On Wed, Jul 13, 2011 at 4:58 PM, case <case.biomaps.rutgers.edu> wrote:
>
>> On Wed, Jul 13, 2011, Erin Kelly wrote:
>>
>> > Apparently the structure looks fine in Pymol--I ran the file through
>> > antechamber and it produced a mol2 file in about 1 second but produced
>> no
>> > sqm.in or sqm.out, is this correct? I've attached the mol2.
>>
>> My guess(?) is that you used the wrong arguments to antechamber, perhaps
>> writing "-bcc" when you meant "-c bcc". If you correctly ask for bcc
>> charges,
>> it should tell you it is running sqm, and take some minutes to complete.
>>
>> ....dac
>>
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>


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Received on Thu Jul 14 2011 - 07:30:02 PDT
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