Hi Gustaf
I work with complex carbohydrates-protein, in this case I have a
pentasaccharide-midkine.
My problem is that the following, to find out which angle / torsion is
the one that is giving me an error, I am launching in the same cluster
(so that the conditions are the same), another compound that has the
same pentasaccharide structure but different conformation of protein
to see the differences in the leap.log and see if there is an error in
the sugar, and by the other hand also another compound that is similar
but different the pentasaccharide structure with the same protein
conformation, to know if the problem comes from the protein. And in
none of these cases does tleap give me this error ... That's why I
don't know what to do anymore ...
Could it be a problem with the docking done earlier?
Thanks in advance,
Myriam
Gustaf Olsson <gustaf.olsson.lnu.se> escribió:
> I suppose that depends on the definition of “wrong”. This is a long
> run with a lot of information so apologies if I might have missed
> something.
>
> First things I find are these:
> glycamod = loadamberparams
> /mnt/netapp1/Store_CSIC/home/csic/car/mtr/myriam/smp-191mkd0syn/parameters/Glycam_06d_mod.dat
> Could not open file
> /mnt/netapp1/Store_CSIC/home/csic/car/mtr/myriam/smp-191mkd0syn/parameters/Glycam_06d_mod.dat: No such file
> or
> directory
>
> modSUBS = loadamberparams
> /mnt/netapp1/Store_CSIC/home/csic/car/mtr/myriam/smp-191mdk0syn/parameters/frcmod.SUBS_lluis
> Loading parameters:
> /mnt/netapp1/Store_CSIC/home/csic/car/mtr/myriam/smp-191mdk0syn/parameters/frcmod.SUBS_lluis
> Modified force field files must contain both a MASS and NONB entry,
> or neither
> Could not load parameter set.
> -- no parameters loaded>>
>
> ##loadOff ions94.lib
> loadOff
> /mnt/netapp1/Store_CSIC/home/csic/car/mtr/myriam/smp-191mdk0syn/parameters/solvents.lib
> Could not open file
> /mnt/netapp1/Store_CSIC/home/csic/car/mtr/myriam/smp-191mdk0syn/parameters/solvents.lib: No such file
> or
> directory
> Could not open database:
> /mnt/netapp1/Store_CSIC/home/csic/car/mtr/myriam/smp-191mdk0syn/parameters/solvents.lib
>
> These things seem like they could be a cause for the missing
> parameters mentioned later on, if these files contains parameters or
> information regarding these particular atoms.
>
>
> I see some "(UNKNOWN ATOM TYPE: )” showing up, this could be a
> potential problem though they do not seem to have anything to do
> with the missing parameters later on..
>
>
> So it seems that whatever you are loading might not get loaded
> properly. I assume this is some additional parameters/modifications
> and might be a cause for the problems observed below?
>
> Warning: Close contact of X.XXXXXX angstroms between
>
> Would indicate that there are things that are either uncomfortably
> close to each other or something has not been defined correctly so
> that “bonded” things have become “unbounded things” that are now way
> too close to each other. In the prior case, an energy minimisation
> of the structure might help remove this warning.
>
> Checking for bond parameters.
> Could not find bond parameter for: OS - CG
> Checking for angle parameters.
> Could not find angle parameter: OS - CG - H2
> There are missing parameters.
>
> This seems self explanatory, either the parameters for the bonds and
> angles were not sourced properly or in an appropriate order, or
> these are not available and would need to be included from an
> external source.
>
> Building bond parameters.
> Could not find bond parameter for: OS - CG
> Building angle parameters.
> Could not find angle parameter: OS - CG - H2
> Building proper torsion parameters.
> ** No torsion terms for OS-CG-OS-CG
> Building improper torsion parameters.
> ** Warning: No sp2 improper torsion term for H-H-N3-H
> atoms are: H1 H2 N H3
>
> I would just probably refer to the statement above.
>
> So potentially you have some things for some atoms defined in some
> of the files which are not getting sourced/loaded properly. This
> could explain the observed complaints. Or, if these are parameters
> for atoms which should be included in a FF, that particular
> parameterset is not being sourced or not sourced correctly. I would
> start by checking which files are missing and not getting loaded and
> if they are important to the warnings presented. In which case
> getting them sourced correctly might solve the problem(s).
>
> If that is not the case, make sure that the parameter files sourced
> do contain the parameters which are reported “missing”. If they do,
> then something is not loaded correctly. If not, you might need to
> look into using different parameters.
>
> I would suspect that this is a good place to start anyway.
>
> Best regards
> // Gustaf
>
>
> On 9 Sep 2020, at 13:50, MYRIAN TORRES RICO
> <myriam.torres.iiq.csic.es<mailto:myriam.torres.iiq.csic.es>> wrote:
>
> Building improper torsion parameters.
> ** Warning: No sp2 improper torsion term for H-H-N3-H
> atoms are: H1 H2 N H3
>
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Received on Thu Sep 10 2020 - 03:00:02 PDT
