Actually I noticed that an oxygen was missing in the sense that the
stoichiometric formula for RET in the pdb file says that there should
be 20 carbons and 1 O but I searched the file repeatedly and couldn't find
an O associated with any of the RET residues. I ran into some trouble at
the next step which may be related to
that.
Woods Halley
On Fri, 1 Aug 2014, Parker de Waal wrote:
> 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 Fri Aug 01 2014 - 18:00:02 PDT
