Re: solution for generating IC

From: Roman Petrenko (rpetrenko_at_gmail.com)
Date: Sat Feb 21 2009 - 22:48:54 CST

You can get an academic license from OpenEye for free and then
download Babel3.3.
After that, assuming you have a PDB file test.pdb run the following:

$ babel -in test.pdb -out test.mopac

$ cat testCA.pdb
ATOM 2 CA ARG A 17 49.758 -12.116 54.808 1.00 99.60 C
ATOM 13 CA ARG A 18 47.760 -9.498 56.717 1.00 96.48 C
ATOM 24 CA ARG A 19 51.091 -7.747 57.186 1.00 96.24 C
ATOM 35 CA GLN A 20 51.876 -7.822 53.466 1.00 89.47 C

$ cat testCA.mopac
AM1

   C 0.00000 1 0.00000 1 0.00000 1 0 0 0
   C 3.80660 1 0.00000 1 0.00000 1 1 0 0
   C 3.79230 1 85.32765 1 0.00000 1 2 1 0
   C 3.80266 1 92.93672 1 52.32581 1 3 2 1

$

i don't know what '1' denotes after each real numbers, but other
numbers are easy to guess: internal coordiantes in the order bond,
angle, dihedral, and indices of atoms forming them.

--
Roman Petrenko
Physics Department
University of Cincinnati
On Sat, Feb 21, 2009 at 6:20 PM, CHINDEA Vlad <vchindea_at_hotmail.com> wrote:
> Hi everybody
>
> Is there a free software available for transforming Cartesian coordinates
> into Internal Coordinates in the format required for CHARMM force field (IC
> statement) ? I guess CHARMM could do it but we do not have it and doing it
> manually it would be quite tediouse.
>
> Many thanks and Best regards
> Vlad Chindea
>
> ________________________________
> What can you do with the new Windows Live? Find out

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