AMBER Archive (2004)

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

From: Jiayun (
Date: Tue Jun 29 2004 - 04:54:46 CDT

Dear Thomas Steinbrecher,

Following the last email, I run the example mm_pbsa and in the
*statistic.out file, all the other data are exactly the same as the example
output except PBSUR, PBCAL, PBSOL, PBELE, PBTOT from Delphi. So obviously,
Delphi didn't run properly. Then I checked the output file. I had
Delphi.prm.eps (binary dielectric map output), Delphi.prm.phi (output binary
potential map) and delphi.prm.log but the file Delphi.prm.pdb (which I guess
is converted from *crd by ambpdb and my ambpdb works fine) and
Delphi.prmout.pdb (output atom coordinate file with radii and charge records
added) were zero. Therefore in "delphi.prm.log", the coordinates couldn't be
read in qdiffxs (see attached delphi.prm.log file).

I found, in mm_pbsa, it runs Delphi via command "Delphi Delphi.prm >

I am not sure whether it could be run this way in my Delphi version. I
attached the script of Delphi. It seems to me that the program runs with
command like "Delphi *.pdb".

I have been trying for a while and still clueless. It will be very helpful
if you could give me more suggestion and possible things to try.

Thanks a lot.












-----Original Message-----

From: [] On Behalf Of
Thomas Steinbrecher

Sent: 23 June 2004 19:09


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




> 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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