If it is not in the parm99.dat file, they might be possible in some other parameter set?
You can always try sourcing another FF, have a look in $AMBERHOME/amber20/dat/leap/cmd. Check the content of any appropriate file and see if the “missing parameters” are there. As I don’t know what you are working on (protein, carbohydrate, other) you might just need a different or an additional set of parameters loaded.
It could also be that the assigned atom names in your structure might not be correct. In this case, changing the atom name to an appropriate substitute for which there are parameters available should solve the problem.
If non of these suggestions seem correct and this is a “novel” interaction, then you need to develop or adapt appropriate parameters to include.
Best regards
// Gustaf
On 9 Sep 2020, at 20:52, MYRIAN TORRES RICO <myriam.torres.iiq.csic.es<mailto:myriam.torres.iiq.csic.es>> wrote:
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<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 Thu Sep 10 2020 - 00:30:03 PDT
