Re: AMBER: problems in adding ACE and NME group

From: backy <backy.ibms.sinica.edu.tw>
Date: Thu, 21 Jun 2007 11:54:47 +0800

If there is a need in placing the whole ACE and NME group, how should I
input their initial coordinations?
Thanks.

backy




----- Original Message -----
From: "David A. Case" <case.scripps.edu>
To: <amber.scripps.edu>
Sent: Wednesday, June 20, 2007 11:41 PM
Subject: Re: AMBER: problems in adding ACE and NME group


> On Wed, Jun 20, 2007, backy wrote:
>
>> Parameter file was not saved.
> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
>
> You had error in the leap step, never actually made a prmtop file.
>
>>
>> ATOM 1 C ACE A 1 70.110 65.868 39.946 1.00 0.00
>> ATOM 2 CA ALA A 1 70.537 66.473 38.657 1.00 0.00
>> ATOM 3 C ALA A 1 69.639 67.664 38.316 1.00 0.00
>> ATOM 4 O ALA A 1 68.434 67.654 38.604 1.00 0.00
>> ATOM 5 CB ALA A 1 70.456 65.436 37.551 1.00 0.00
>> ATOM 6 N THR A 2 70.232 68.687 37.711 1.00 0.00
>> ATOM 7 CA THR A 2 69.495 69.875 37.320 1.00 0.00
>> ATOM 8 C THR A 2 69.540 70.004 35.797 1.00 0.00
>
> You have to add an entire ACE residue (or at least the heavy atoms), not
> just
> one C atom. Also, you have two residues labelled "1" (ACE and ALA), which
> will confuse LEaP. Also, there is no N atom for the ALA.
>
> Don't try to run sander until you get LEaP running the way it should.
>
> ...good luck...dac
>
> p.s.: are you sure you want to add the capping groups to a complete
> protein?
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Received on Sun Jun 24 2007 - 06:07:19 PDT
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