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-- Amy He Chemistry Graduate Teaching Assistant Hadad Research Group Ohio State University he.1768.osu.edu<mailto:he.1768.osu.edu> From: Robert Heße via AMBER <amber.ambermd.org> Date: Wednesday, May 31, 2023 at 8:32 AM To: Carlos Simmerling <carlos.simmerling.gmail.com> Cc: amber.ambermd.org <amber.ambermd.org> Subject: Re: [AMBER] Negative barrier term when fitting with mdgx Am 2023-05-31 14:19, schrieb Carlos Simmerling: > I can't comment on whether the numbers you are getting are accurate, > but in principle there is nothing wrong with a negative amplitude > term. these are not "barriers" since they are simply corrections terms > to the underlying model. it is quite reasonable that sometimes the > barrier in the underlying model is too large, and needs to be reduced. > it is a common misconception that the dihedral terms are the > rotational energy profile - they are not. they are just corrections. > > On Wed, May 31, 2023 at 8:11 AM Robert Heße via AMBER > <amber.ambermd.org> wrote: > >> 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 >> >> _______________________________________________ >> AMBER mailing list >> AMBER.ambermd.org >> https://urldefense.com/v3/__http://lists.ambermd.org/mailman/listinfo/amber__;!!KGKeukY!2cZAFr5vu-jyyZe_ij1zIifFLJj48gk-NjdDe-NKZFMBAlLKcbcg9xlptqp6P-ZA6dQY9KlLDtz1xhbNtsDiqj_S28g$<https://urldefense.com/v3/__http:/lists.ambermd.org/mailman/listinfo/amber__;!!KGKeukY!2cZAFr5vu-jyyZe_ij1zIifFLJj48gk-NjdDe-NKZFMBAlLKcbcg9xlptqp6P-ZA6dQY9KlLDtz1xhbNtsDiqj_S28g$> Thank you for the fast response! This is at least reassuring to know but they still seem quite large compared to other parameters im Amber. If im not mistaken terms with 20+ kcal/mol were usually with sulfur or phosphor bounds. Compared to previous fits i did with mdgx, that seems a bit odd. What would be the best way to verify my parameters? With best regards, Robert Heße _______________________________________________ AMBER mailing list AMBER.ambermd.org https://urldefense.com/v3/__http://lists.ambermd.org/mailman/listinfo/amber__;!!KGKeukY!2cZAFr5vu-jyyZe_ij1zIifFLJj48gk-NjdDe-NKZFMBAlLKcbcg9xlptqp6P-ZA6dQY9KlLDtz1xhbNtsDiqj_S28g$<https://urldefense.com/v3/__http:/lists.ambermd.org/mailman/listinfo/amber__;!!KGKeukY!2cZAFr5vu-jyyZe_ij1zIifFLJj48gk-NjdDe-NKZFMBAlLKcbcg9xlptqp6P-ZA6dQY9KlLDtz1xhbNtsDiqj_S28g$> _______________________________________________ AMBER mailing list AMBER.ambermd.org http://lists.ambermd.org/mailman/listinfo/amberReceived on Wed May 31 2023 - 08:30:04 PDT