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
On Thu, 31 Jul 2014, Jason Swails wrote:
> On Thu, Jul 31, 2014 at 5:47 PM, J.W. Halley <woods.woods1.spa.umn.edu>
> wrote:
>
>>
>> Warning: detected more than 10 Residue sequence numbers;
>> this may be a large multiple residue PDB file;
>> large multiple residue PDB files are not supported.
>> Continuing, but problems may be encountered.
>> Segmentation fault
>>
>> Certainly my file contains more than 10 residues. Am I supposed to
>> generate a separate pdb file for the RET and CLR residues? I certainly
>> don't know how to do that.
>
>
> Yes, you are supposed to generate a separate PDB file for RET and another
> for CLR and parametrize each of those compounds separately.
>
> Doing so is easy. Open the PDB file up your favorite text editor. Copy
> the lines containing the atoms in the RET residue and paste them into a new
> file. Do the same thing with CLR.
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Thu Jul 31 2014 - 17:30:02 PDT
