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 Wed Sep 09 2020 - 05:30:04 PDT
