Also you're missing an oxygen molecule.
Parker
________________________________________
From: Jason Swails [jason.swails.gmail.com]
Sent: Thursday, July 31, 2014 10:49 PM
To: AMBER Mailing List
Subject: Re: [AMBER] this a very green neophyte's question.
On Thu, Jul 31, 2014 at 8:29 PM, J.W. Halley <woods.woods1.spa.umn.edu>
wrote:
>
> Thanks, but a question about a detail. Are, for example, the following
> lines enough for RET or does the pdb file need some more structure? Thanks.
>
> HETATM 7029 C1 RET A 301 19.065 -6.565 17.148 1.00 4.14
> C
> HETATM 7030 C2 RET A 301 19.236 -7.645 16.023 1.00 2.80
> C
> HETATM 7031 C3 RET A 301 19.563 -7.208 14.682 1.00 2.90
> C
> HETATM 7032 C4 RET A 301 20.528 -6.055 14.582 1.00 2.77
> C
> HETATM 7033 C5 RET A 301 20.377 -4.947 15.610 1.00 3.73
> C
> HETATM 7034 C6 RET A 301 19.696 -5.117 16.835 1.00 4.92
> C
> HETATM 7035 C7 RET A 301 19.670 -3.895 17.795 1.00 6.36
> C
> HETATM 7036 C8 RET A 301 19.087 -3.742 19.006 1.00 8.08
> C
> HETATM 7037 C9 RET A 301 19.202 -2.643 19.966 1.00 10.47
> C
> HETATM 7038 C10 RET A 301 18.436 -2.736 21.105 1.00 11.53
> C
> HETATM 7039 C11 RET A 301 18.350 -1.829 22.240 1.00 12.69
> C
> HETATM 7040 C12 RET A 301 17.490 -2.061 23.245 1.00 13.79
> C
> HETATM 7041 C13 RET A 301 17.241 -1.239 24.453 1.00 14.11
> C
> HETATM 7042 C14 RET A 301 16.216 -1.643 25.271 1.00 16.18
> C
> HETATM 7043 C15 RET A 301 15.589 -0.983 26.436 1.00 18.38
> C
> HETATM 7044 C16 RET A 301 19.180 -7.197 18.520 1.00 4.54
> C
> HETATM 7045 C17 RET A 301 17.542 -6.396 17.061 1.00 4.67
> C
> HETATM 7046 C18 RET A 301 21.088 -3.671 15.162 1.00 2.94
> C
> HETATM 7047 C19 RET A 301 20.137 -1.475 19.715 1.00 11.49
> C
> HETATM 7048 C20 RET A 301 18.018 0.037 24.683 1.00 12.68
> C
>
For many programs (antechamber included), this should be fine.
Of course you could always try it yourself and see. If files are wrong,
you will usually see programs fail with an error message (not always a
helpful error message, unfortunately).
I encourage you to try stuff for yourself -- it's the best way to learn
(especially when things go wrong and you figure out how to fix them). It's
often more time effective to try this type of thing rather than try and
consult experts to ensure it will be right before trying.
Good luck,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Thu Jul 31 2014 - 20:30:04 PDT
