Re: Help needed about mm_pbsa

From: Holger Gohlke <>
Date: Thu 15 Aug 2002 10:04:03 -0700


I cannot provide a complete answer from your information yet, but
several things might be helpful:

* Could you please check if crd files with the (according to the info in
your mm_pbsa script) name
"try_GB_new_{_protein, _ligand, _complex}.crd.#" where "#" is a number
were generated by your run?
* If not, how does your "md5_crd1.inpcrd" file look like? make_crd
requires a crd file from a sander run, i.e. a file with a title line at
the beginning and then 10 columns of coordinates,
not 6 as in restrt files. As you decribe that your file has two lines -
a title and a single number - I expect it to be a restrt file?

> By the way, for the crd files as input, can I use restrt files from MD
> simulations directly (with water),
I think, _technically_ you could since snapshot files generated by
make_crd have the same format as restrt files generated by sander
(except for information about velocities and perhaps box information).
But: unless you have a good explanation why single water molecules might
be considered to belong to the solute and not to the solvent, there
should be no reason to include explicit water molecules into a
calculation applying a continuum representation for the solvent (at
least not in the first trial ...).

> or should I use the crd file from leap, in
> this latter route, I ptraj restrt files to pdb files (stripping out water) and
> then make crd file from pdb files in leap (this only contain proteins, not
> water).
Either that way or feed your trajectory through make_crd and extract
snapshots at certain time steps.

> Also IN the crd file, The first two lines are one empty line, one line
> with numbers indicating how many atoms in the system. Can the remove_title_line
> automatically remove these two line?
remove_title_line only removes the title line. You apply the wrong file
format here, use your crd files in this case (see above).

I hope this gives a first starting point - best regards


Dr. Holger Gohlke
Dept. of Molecular Biology, TPC15
The Scripps Research Institute
10550 N. Torrey Pines Rd.
La Jolla CA 92037  USA
phone: +1-858-784-9788
fax:   +1-858-784-8896
Received on Thu Aug 15 2002 - 10:04:03 PDT
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