I am very happy to hear that it resolved itself.
Do check everything one more time or two, you do not want to end up finding an issue 3-6 weeks later.
Best regards
// Gustaf
> On 16 Sep 2020, at 10:17, MYRIAN TORRES RICO <myriam.torres.iiq.csic.es> wrote:
>
> Hi Gustaf,
>
> I think that the problem is solved. I returned to load the paremeters
> files, and now it works! Thanks you so much for your time.
>
> Best regards
>
> Myriam
> Gustaf Olsson <gustaf.olsson.lnu.se> escribió:
>
>> Hello Myrian
>>
>> I tried reaching out directly as I suspected that this might not be
>> of “general interest” though I am unsure if that email reached you
>> since there was apparently some problem with my organisations email
>> services during the weekend.
>>
>> I see an issue with the files you sent. Leap complains about groups
>> including an OS atom. I am unable to find this atom in either of the
>> attached files. This means that either the PDB files attached are
>> not the right ones (the ones creating problems in leap) or there is
>> a problem assigning atom names/types for some reason. If you are
>> still experiencing problems and then if possible, could you send the
>> topology and coordinate files for the structures with problems.
>>
>> Best regards
>> // Gustaf
>>
>> On 11 Sep 2020, at 12:46, MYRIAN TORRES RICO
>> <myriam.torres.iiq.csic.es<mailto:myriam.torres.iiq.csic.es>> wrote:
>>
>>
>> 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<mailto: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><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><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><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 Wed Sep 16 2020 - 02:30:02 PDT
