Hi Gustaf,
First of all thank you for your time with me.
I keep trying everything that you tells me, but the pdb files that I
put in leap are still exactly the same in my eyes. If it's not much of
a hassle, I've attached the .pdb files which I'm working with in
tleap, for a second view. The angle / torsion that gives me an error,
seems to correspond to Galactosamine, C4 and C6 ... but visually there
does not seem to be any wrong link ...
The mdk2_rig.pdb this the problem file, and the md4rig.pdb the correct
file. The only difference is the
protein conformation (midkine-2 and midkine-4).
thanks in advance again,
Myriam
Gustaf Olsson <gustaf.olsson.lnu.se> escribió:
> Just to set the stage, I am assuming that “different protein
> conformation” means structure is different though AA sequence is the
> same.
>
> Both of these to examples lists works:
> Same sugar - Different protein conformation
> Different sugar - Same protein conformation
>
> If my assumption is correct, then there should be no problem with
> parameters for the sugar or the protein as they are covered by the
> combination:
>
> Same sugar - Same protein conformation
>
> What’s next?
>
> Do a visual inspection using xLEaP edit mode, VMD or something
> similar with a GUI. What is the group that “CG - OS - S - O” refers
> to? This seems to be the last “unknown” group and if you solve this
> then the problem should be solved.
>
> Is this group present in the working example files (should
> realistically not be present if they do not produce the same
> errors). Then what has changed? If this is a product of the export
> process from docking then correcting the labels to match those in
> the working examples should solve this issue.
>
> If these atoms are present in the other files it is possible that
> protonation stages has changed or something regarding their
> positions/coordinates so that they are interpreted as bonded though
> should not be. Make sure that the group is interpreted correctly
> when loaded into leap.
>
> At least a place to start
>
> Best regards
> // Gustaf
>
>
> On 10 Sep 2020, at 11:38, MYRIAN TORRES RICO
> <myriam.torres.iiq.csic.es<mailto:myriam.torres.iiq.csic.es>> wrote:
>
> 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<mailto: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><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 Fri Sep 11 2020 - 04:00:02 PDT
