David A. Case wrote:
> Note that changing the prmtop specs would require changes to many
> external programs (such as VMD), in addition to whatever changes would
> be needed in Amber itself. We probably don't even know all the programs
> that read prmtop files. So, we should be conservative here, and require
> a really good reason for any changes.
So, the important thing is to better document the format so any code
that read them will be better at handling potential changes in the
future. My guess is:
1) All lines limited to 80, including comments.
2) Lines may be blank-trimmed to less than 80 columns, except for string
arrays (there is more chance of error here).
3) To allow for the future addition of more informaitonal tags, I/O
routines should tolerate any additional lines beginning with '%'
followed by an unrecognized tag, and essentially treat them as %COMMENT
lines.
> p.s. Joe: I now have a collaboration with a crystallographer who has
> about a dozen chains in her structures. Do you have a procedure that
> would (a) update a prmtop file to include original residue numbers and
> chain ID's, (b) allow ambpdb to use such information?...thanks!
Here is the status, for anyone who wants to try it.
In src/xray is a program add_pdb. Given a PRMTOP from leap, and the
matching source PDB file, it will add residue and atom information to
the PRMTOP file. It assumes that you have not done any special editing
that would reorder any residues, and that all extra residues are bulk
solvent. It uses simple command-line args, and has a built-in help message.
It will add element data to the PRMTOP, which is taken from the
right-hand column present on newer PDB files. Otherwise, it assumes
proper PDB v2 element-aligned atom names. There is a "-guess" flag,
which means to guess element types only by name when element info is
missing (maybe it should be "-unaligned")
I have modified the ambpdb to accept a new argument "-ext", which means
it should use the new extended PRMTOP info to create the PDB file. For
now, it automatically excludes any of the extra residues assumed to be
bulk solvent.
Joe
_______________________________________________
AMBER-Developers mailing list
AMBER-Developers.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber-developers
Received on Sun Apr 12 2009 - 01:10:01 PDT
