Dear Professor Case,
Yes, I did set head and tail.
But I found it was not enough.
The Prepin Files I made have wrong connect information.
I succeed to avoid the anomalous TER
When I used MOL2 files.
Anyway, I will send the files and script
To your e-mail address.
Yours sincerely,
Ikuo KURISAKI
-----Original Message-----
From: David A Case [mailto:case.biomaps.rutgers.edu]
Sent: Wednesday, March 06, 2013 12:56 AM
To: AMBER Mailing List
Subject: Re: [AMBER] Annomalous "TER" is inserted in a peptide including
non-standard AA
On Tue, Mar 05, 2013, kurisaki wrote:
>
> Using "desc" command,
> I found that connection0/1 was not properly set, Exactly, when I used
> PREP file.
>
> Such a connection was not set at all
> When I used MOL2 files.
But you also said that you "set the head and tail for these residues". Can you
say exactly what you did, and in what order, e.g. give the exact commands you
used in LEaP? It looks like there may be a bug, either in the documentation or
in the code, and we should try to fix it. This is much easier if you can
provide a small example that illustrates the problem.
...thanks...dac
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Received on Tue Mar 05 2013 - 17:00:02 PST
