AMBER Archive (2004)

Subject: RE: AMBER: a question on MM-PBSA and Delphi

From: Thomas Steinbrecher (
Date: Wed Jun 23 2004 - 13:09:16 CDT


> I had only one link "fort.13 -> ras_raf_II_wt_com.pdb.1" generated. The
> ras_raf_II_wt_com.all.out file is like

Thats ok, mm_pbsa generates only the links it needs for the next snapshot.

> So it seems Delphi didn't work properly. Then I used the same pdb file to
> make two copies: one is called *.pdb and the other is *pdb.1 to run Delphi
> directly. The Delphi with *.pdb file gave the output and generated a new pdb
> with the assigned atomic radius and charge of each atom placed in columns
> 55-60 and 61-67 but the other one with the name *pdb.1 didn't generate the
> new pdb file. So that's why I sent the first email, saying I think Delphi

Since I have only worked with Delphi4, I cannot tell you if this behaviour
is to be expected, but it should not be a problem while running MM-PBSA,
since Delphi only gets a file named fort.13 as input.

I would suspect something else is wrong with your Delhi runs. Do you get a
partial output file from Delphi with a more informative error message?



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