Dear Amber users and developers,
I am reposting my request since unfortunately I did not receive any feedback.
I would like to use mdgx to refine the estimate of the force field terms related to the torsional barriers along the backbone of a polymer. I am using a tetramer as reference system.
I created a library with monomer units, properly assigning atom types, charges, head and tail atoms.
I am following the mdgx tutorial available on Amber website. In particular, I try to fit the terms related to three different torsions. In terms of gaff2 atom types, they are the following:
c3 c os c3
c os c3 c
os c3 c os
I computed the energies of about 500 structures and I have successfully created the files containing the coordinates and the energies. When I try to perform the fit, I receive the following message:
mdgx >> Unique adjustable parameters enumerated.
mdgx >> 564 conformations read.
mdgx >> Parameter keys read.
mdgx >> Torsion type os c3 c os marked for optimization but not found
mdgx >> in any systems.
mdgx >> Torsion type c os c3 c marked for optimization but not found
mdgx >> in any systems.
Essentially, the code says that two out three torsions are not present, but they are. I did another check, creating a mol2 file of the tetramer and using parmchk to print the entire parameter set (using the option -a 'Y'). The resulting .frcmod file confirms that the torsions are indeed present. This is the input file for fitting (I copied gaff2.dat in the directory where I am performing the fitting):
&files
-parm gaff2.dat
-d PLL.dat
-o fit.out
&end
¶m
System PLL.top coords.cdf energies.dat
ParmOutput frcmod
eunits hartree
accrep report.m
verbose 1
fith os c3 c os
fith c3 c os c3
fith c os c3 c
hrst 0.0002
&end
Am I missing something?
I thank in advance for the support.
Tommaso
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Received on Mon Jan 10 2022 - 00:00:02 PST
