Makoto Yoneya wrote:
Dear GROMACS users:
I found the following in ML archive about the box vectors entry in "gro"
file.
doing:
% editconf -f <in.pdb> -o <out.gro> -bf tric -box a b c -angles bc ac
ab
the last line of out.gro looks like:
1.12020 0.92620 6.259008 0.00000 0.00000 0.00000 0.00000 -0.99134
0.00000
what are these 9 values in this case? (angles, unit cell vectors..) why
nine?
They are the XX YY ZZ XY XZ YX YZ ZX ZY components of the three box
vectors. The ordering is a bit counterintuitive, but that is because it
keeps the XX YY ZZ 'cubic' part of the box vectors in the beginning, so
it corresponds to the case where only the three box-edge lengths are
defined for a cubic box.
Could someone kindly teach me the exact translate formulas from PDB file
CRYST1
entry of "a, b, c, alpha, beta, gamma"
to the gro file entry "XX YY ZZ XY XZ YX YZ ZX ZY" above?
Thank you for advance.
Makoto Yoneya, Dr.
AIST, Japan
Hi Makoto,
three of these values are always zero, so there really are only six
variables as it should be. This is due to some stupid error 15 years ago
and now we have to be backwards compatible with our old gro files.
You can just try it with a pdb file that has a = b = c = 1 and alpha
beta gamma as you like it.
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