Re: AMBER: problems in adding ACE and NME group

From: backy <backy.ibms.sinica.edu.tw>
Date: Thu, 21 Jun 2007 12:00:39 +0800

by the way, this complete protein is a test case for me practicing the
protein capping stuff.
:)
backy

----- Original Message -----
From: "backy" <backy.ibms.sinica.edu.tw>
To: <amber.scripps.edu>
Sent: Thursday, June 21, 2007 11:54 AM
Subject: Re: AMBER: problems in adding ACE and NME group


> 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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>>
>> --
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>> Version: 7.5.472 / Virus Database: 269.9.1/854 - Release Date: 2007/6/19
>> U 01:12
>>
>>
>
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Received on Sun Jun 24 2007 - 06:07:21 PDT
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