Jones de Andrade wrote:
>From .gro or .pdb file in the standard way.
> number of molecules types,
No
> number of molecules of each type,
No
> number of atoms of each molecule type,
No
I think those three can become yes in a really easy way: some kind of
"state machine" would easily do the trick and "count" them properly.
Yes, but now you have to infer molecule changes from residue name
changes, which is doable, but messy.
> coordinates,
Yes
From .xtc or .pdb file.
charges
Yes, if you use the right editconf option
and masses on a .pdb file, correct?
No.
Only modifying editconf to print those in a adapted .pdb file, throw a
file conversion and much disk space "wasted". Or I can learn exactly
from editconf how to read it from .tpr or .top (I guess it takes from
these files the atomic charges when needed) and adapt into my codes.
The point of editconf is to feed your system *one* pdb structure with
atom names, charges and/or whatever - it would be easy to modify
editconf to write masses in one column and charges in another. You rely
on the user to then supply a .xtc file that corresponds to that .pdb, in
the same way that most of the GROMACS analysis tools accept an .xtc and
various subsets of the possible structure files. You don't convert your
.xtc to a .pdb trajectory, because that would be immensely wasteful, and
the static information of the names, masses and charges doesn't vary
with time under the MD approximation.
If you use the editconf suggestion to get charges, you don't need to
read a .tpr file.
But then or I get locked into the problem of generality of having too
much disk usage. But that idea will be also usefull to learn how to read
the masses and charges from .tpr files.
Easier is to hack editconf as described above.
Mark
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