Re: AMBER: LoadPdb Error: In file [chirality.c], line 121 Message: Atom C67 is not in the first list

From: David A. Case <case.scripps.edu>
Date: Wed, 16 Nov 2005 08:56:44 -0800

On Tue, Nov 15, 2005, Ilyas Yildirim wrote:
>
> I am getting the same error what Nithin is getting. Here is what I have
> done and the error I am getting:
>
> [yildirim.anatolia ~/nithin]# ls -l
> total 68
> -rw-r--r-- 1 yildirim users 16271 2005-11-15 23:37 leap.log
> -rw-r--r-- 1 yildirim users 6284 2005-11-15 23:35 popc.frcmod
> -rw-r--r-- 1 yildirim users 20933 2005-11-15 23:35 popc.pdb
> -rw-r--r-- 1 yildirim users 10380 2005-11-15 23:35 popc.prepin
> -rw-r--r-- 1 yildirim users 134 2005-11-15 23:37 test.in
> -rw-r--r-- 1 yildirim users 225 2005-11-15 23:37 test.in~

I have slightly different file sizes:

-rw------- 1 case None 6162 Nov 10 08:54 popc.frcmod
-rw------- 1 case None 20655 Nov 10 08:54 popc.pdb
-rw------- 1 case None 10219 Nov 10 08:54 popc.prepin
-rw-rw-r-- 1 case None 131 Nov 16 08:44 test.in

I don't remember making any changes, but I can't seem to get the mail archives
to cough up the original attachments... Can you send me (privately) your
files?

Anyway, it is great that you can reproduce this, since you have a chance to
debug it. I've tried this on several machines, using Amber 7, 8 and 9, and
never seen any failures. So there is not much more I can do.

....dac

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Received on Wed Nov 16 2005 - 17:53:00 PST
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