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
This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:52:23 CST