Jones de Andrade wrote:
Hi Mark.
Wait a second, you mean that editconf would allow me to have both
charges and masses on a .pdb file directly from command line (having
other matters asking for my presence absolutelly now, so please forgive
me if this message becomes somehow strange)
So, I would have atom names, number of molecules types, number of
molecules of each type, number of atoms of each molecule type,
coordinates, charges and masses on a .pdb file, correct?
no just atoms and charges.
But, still, where could I then easilly get the box type and sizes, as
well as simulation times?
box is in xtc file.
You could make your life easier by learning some C, unless you hae to
link the trajectories to a big fortran library. By the way you can also
trjconv -f k.xtc -o l.g87 which you can read using 10f8.3
Thanks a lot for all the help, and sorry for this punctual hurry here.
Sincerally yours,
Jones
On 9/30/07, *Mark Abraham* < [EMAIL PROTECTED]
<mailto:[EMAIL PROTECTED]>> wrote:
David van der Spoel wrote:
> the box is in the xtc file, if you need the atom names a
corresponding
> pdb or gro file should do the trick. don't try to read tpr files or
> gmxdumps of it, that's a complete waste of time. you can e.g. use
> editconf to dump a pdb file with charges in the b-factor fields.
Yes, I now see that editconf has that ability, and Jones can fill in the
masses himself, so he doesn't need to parse the .tpr at all.
> And indeed, using fortran will make your life quite miserable for
these
> kind of things.
:-)
Mark
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David van der Spoel, Ph.D.
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755.
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