[AMBER] Problems with mdgx torsion parameters fitting - possible bug with polymers?

From: Casalini Tommaso <tommaso.casalini.chem.ethz.ch>
Date: Mon, 10 Jan 2022 07:51:49 +0000

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):

 -parm gaff2.dat
 -d PLL.dat
 -o fit.out

 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


Am I missing something?

I thank in advance for the support.

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Received on Mon Jan 10 2022 - 00:00:02 PST
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