Waiting for the average structure

HADDOCK
1

I’m rerunning haddock runs from the webserver locally with modified params,
but all hang at the ‘waiting for the average structure…’ point after all it1
structures are calculated (before water) file.list/nam/cns are made.

also, is there a param determining the # of structures in it1 (400) or
is this hardcoded?? there’s no 400 in run.cns

E

2

Dear Eiso,

Unfortunately I cannot answer to your first question, it is not a situation I encountered previously…

However, for your second question, there is indeed a parameter that indicates the number of structures generated in it1, it is called “structures_1”(“structures_0” for it0 and “structures_2” or “waterrefine” for water) and must appear in all run.cns files as far as I know. Not sure if the lack of this parameter in your run.cns could have led to the issue you have but you should still check for it…

Did you try to run the same job (with the modified parameters) through the webserver?

Good luck,

Mikael

3

mtrellet http://ask.bioexcel.eu/users/mtrellet
August 3

Dear Eiso,

Unfortunately I cannot answer to your first question, it is not

It looks like I left too many files in it1/analysis (complex_ave.pdb & some
.lis files)
now it’s running again.

a situation I encountered previously…

However, for your second question, there is indeed a parameter that
indicates the number of structures generated in it1, it is called "
structures_1"(“structures_0” for it0 and “structures_2” or
“waterrefine” for water) and must appear in all run.cns files as far as I
know. Not sure if the lack of this parameter in your run.cns could have led
to the issue you have but you should still check for it…

Did you try to run the same job (with the modified parameters) through the
webserver?

It’s originally a job from the webserver but the topology params are not
good.
So it’s not possible to do it on the webserver with the modified params.

the run.cns is directly from the webserver (with some modified paths) so
the 400

run.cns says:

{===>} structures_0=1000;
{===>} structures_1=200;
{===>} waterrefine=200;

but still 400 .pdb files are generated

in the it1 dir there are
400 complex_#.pdb (#=1…400) and
200 complex_#.pdb0 (#=401_600) and
200 complex_#.pdb0_1 (#=201_400)
files

Not sure if these _1 files are normally supposed to be made…
If I’m correct this usually means something has been redone.

Is there an explanation somewhere of this part of the protocol?

Eiso

4

in the it1 dir there are
400 complex_#.pdb (#=1…400) and
200 complex_#.pdb0 (#=401_600) and
200 complex_#.pdb0_1 (#=201_400)
files

Something seems strange with your local setup… The pbd0 files are temporary files that should have been removed once the pdb files appear

The _1 files mean you must have run haddock twice… CNS does not overwrite a file in principle, but adds a _1, _2… at the end of it for the previous versions.

5

this is not (only) happening in a local run but on the haddock server
(I just unpacked the tgz of the run again to be sure.)

should I send you a haddockparam.web to check?

Eiso

6

Yes please, I can have a look at it.

7

Alex already answered.
rotate180_2 was the culprit.

setting it to False solved the issue.

E

Mikael Trellet wrote: