Re: [AMBER] error tleap

From: MYRIAN TORRES RICO <myriam.torres.iiq.csic.es>
Date: Wed, 09 Sep 2020 20:52:24 +0200

Thank you so much,
I had been trying some of the things you have told me and now the
error is this (it is still related to not finding certain angles /
torsions):

Checking Unit.
Building topology.
Building atom parameters.
Building bond parameters.
Building angle parameters.
Could not find angle parameter: OS - S - O
Could not find angle parameter: OS - S - O
Could not find angle parameter: OS - S - O
Could not find angle parameter: OS - S - O
Could not find angle parameter: OS - S - O
Could not find angle parameter: OS - S - O
Could not find angle parameter: OS - S - O
Could not find angle parameter: OS - S - O
Could not find angle parameter: OS - S - O
Could not find angle parameter: OS - S - O
Could not find angle parameter: OS - S - O
Could not find angle parameter: OS - S - O
Could not find angle parameter: OS - S - O
Could not find angle parameter: OS - S - O
Could not find angle parameter: OS - S - O
Could not find angle parameter: OS - S - O
Could not find angle parameter: OS - S - O
Could not find angle parameter: OS - S - O
Building proper torsion parameters.
  ** No torsion terms for CG-OS-S-O
  ** No torsion terms for CG-OS-S-O
  ** No torsion terms for CG-OS-S-O
  ** No torsion terms for CG-OS-S-O
  ** No torsion terms for CG-OS-S-O
  ** No torsion terms for CG-OS-S-O
  ** No torsion terms for CG-OS-S-O
  ** No torsion terms for CG-OS-S-O
  ** No torsion terms for CG-OS-S-O
  ** No torsion terms for CG-OS-S-O
  ** No torsion terms for CG-OS-S-O
  ** No torsion terms for CG-OS-S-O



I have looked for these angles / torsions in the parm99.dat file to
add them to my own as you have told me before, but I cannot find these
in particular ... how do I do it then?

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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> AMBER.ambermd.org
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Received on Wed Sep 09 2020 - 12:00:02 PDT
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