[AMBER] Negative barrier term when fitting with mdgx

From: Robert Heße via AMBER <amber.ambermd.org>
Date: Wed, 31 May 2023 14:06:31 +0200

Dear AMBER user,

recently i wrote to this mailing list regarding the fitting of missing
atom types for modified nucleotides and after some tries i was able to
generate a frcmod file, which takes into account both Gaff and
AMBER(/OL15) atom types. When i wanted to refine these mixed parameters
with mdgx, i encountered negative barrier terms: 
----
Generated by mdgx executing 07_fit.mdgxin.
MASS
BOND
ANGL
DIHE
OS-CT-na-cc   1    46.06460    0.0 -2.0  same as X -c3-na-X , penalty 
score= 0.0, Fit by mdgx
OS-CT-na-cc   1     1.57990    0.0  1.0  same as X -c3-na-X , penalty 
score= 0.0, Fit by mdgx
OS-CT-na-ca   1   -30.72963    0.0 -2.0  same as X -c3-na-X , penalty 
score= 0.0, Fit by mdgx
OS-CT-na-ca   1    34.91051    0.0  1.0  same as X -c3-na-X , penalty 
score= 0.0, Fit by mdgx
CT-CT-na-cc   1    41.14259    0.0 -2.0  same as X -c3-na-X , penalty 
score= 0.0, Fit by mdgx
CT-CT-na-cc   1    10.25461    0.0  1.0  same as X -c3-na-X , penalty 
score= 0.0, Fit by mdgx
CT-CT-na-ca   1   -28.74262    0.0 -2.0  same as X -c3-na-X , penalty 
score= 0.0, Fit by mdgx
CT-CT-na-ca   1    54.87103    0.0  1.0  same as X -c3-na-X , penalty 
score= 0.0, Fit by mdgx
H2-CT-na-cc   1    39.28179    0.0 -2.0  same as X -c3-na-X , penalty 
score= 0.0, Fit by mdgx
H2-CT-na-cc   1     5.71388    0.0  1.0  same as X -c3-na-X , penalty 
score= 0.0, Fit by mdgx
H2-CT-na-ca   1   -32.28837    0.0 -2.0  same as X -c3-na-X , penalty 
score= 0.0, Fit by mdgx
H2-CT-na-ca   1    49.39032    0.0  1.0  same as X -c3-na-X , penalty 
score= 0.0, Fit by mdgx
IMPROPER
NONB
----
Those dihedral are for C2'/O4'/H1'-C1'-N9-C4/C8 of a modified 
deoxyguanosine nucleotide. I tried to adjust the Tutorial for mdgx for 
this as much as possible. I generated a total of 144 structures (2.5°) 
for sampling and then performed single point calculations via Orca. The 
Orca runs terminated normally and extracting the energies via the Speval 
Module went successful as well. The fitting report from the mdgxout-file 
also looked good, showing an improvement of the parameters:
(1.) Energies of each system, according to the fitted parameters.  Units 
on
      errors are kcal/mol.  The original model's energies are compared to
      target energies after applying an offset to make the average of 
each set
      of energies for any given system equal (see Section 3).
                       RMS Error         Correlation    Fitted   Fitted   
Model
       System        Orig    Fitted    Orig    Fitted   Terms    Energy   
Diff.
  ----------------  -------  -------  -------  -------  ------  -------  
-------
  /home/hesse/DNAz   8.1688   1.5465   0.0562   0.9795      12     0.00   
  8.010
<++>-----------------------------------------------------------------------<++>
Sorry for the detailed information so far but im a but confused by the 
generation of negative energy barriers as i couldn't find a mistake in 
the files so far.
With best regards,
Robert Heße
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Received on Wed May 31 2023 - 05:30:02 PDT
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