extracting real numerical values for steric energies
Hello, I'm using Chimera to optimize the structures of several small-molecule transition metal complexes. The goal is to compare the steric energies of different diastereomers. I 've searched the local documentation on version 1.11.2 (Macintosh) for the term "Minimize structure" but found nothing which actually described the meaning,number format, reference points and units which are produced by the "Minimize Structure" command and appear in the "Reply log". For example, the potential energy values which are returned can be either < 0 or > 0 (!!) If a minimization is occurring, then the force field will describe those parameters - but the preceding values make no sense. Some advice and instruction would be appreciated. Thanks *Dr. Fenton Heirtzler* ------------------------------- Phone: +1-301-312-5145 LinkedIn <http://www.linkedin.com/in/fentonhorgchem/>
Hello Dr. Fenton Heirtzler, I agree it can be difficult to find specifics amongst a lot of text. I don’t know if this is what you meant, but from the “Minimize Structure” page: <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/minimize/minimize....> "Energies (kJ/mol) are reported in the Reply Log. **Step numbers reported by MMTK are 2 greater than the actual numbers of minimization steps performed. The additional “steps” are not minimization steps but operations required to obtain gradient values and updated coordinates.**” As I understand it there is no energy decomposition available directly from MMTK to Chimera, and thus only the total energy is reported. Total energies may be positive or negative depending on whether the positive interactions outweigh the negative interactions and conformational strain. As there is no decomposition, there is no way to tell how much of the total is from the strain vs. nonbonded interactions, or electrostatic vs. VDW interactions. That said, my understanding is that simple molecular mechanics with atoms as nonpolarizable point charges is unlikely to provide an accurate representation of transition metal complexes, and Antechamber parametrization was not developed to handle such cases. This reply from several years ago somewhat addresses this issue, although the URL within it is no longer valid: <http://www.cgl.ucsf.edu/pipermail/chimera-users/2007-June/001665.html> In short, you may need to use some other program to accurately model these situations. I hope this clarifies the situation, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jun 5, 2017, at 11:04 AM, Fenton Heirtzler <heirtzlerchempro@gmail.com> wrote:
Hello, I'm using Chimera to optimize the structures of several small-molecule transition metal complexes. The goal is to compare the steric energies of different diastereomers.
I've searched the local documentation on version 1.11.2 (Macintosh) for the term "Minimize structure" but found nothing which actually described the meaning,number format, reference points and units which are produced by the "Minimize Structure" command and appear in the "Reply log".
For example, the potential energy values which are returned can be either < 0 or > 0 (!!)
If a minimization is occurring, then the force field will describe those parameters - but the preceding values make no sense.
Some advice and instruction would be appreciated.
Thanks Dr. Fenton Heirtzler
Hello Dr. Meng, Thanks for your explanations on this. Yes, of course Chimera really isn't even intended to handle the sort of molecules of interest. The transition metal complexes have organic ligands with asymmetric centers attached. The idea was to compare the ligand steric interactions while considering the point chirality about the central tetrahedral copper(I) center. Not so much molecular orbitals or electronics. As an organic chemist, I'm more accustomed to seeing energies having positive values, i.e. stability increases as energy drops. Since Chimera optimizes according to energies becoming increasingly negative, then it looks like you're using the opposite scale. For example, for -20 vs -14 kJ/mol , -20 is more stable than -14. Thanks again and have a nice evening. Fenton *Dr. Fenton Heirtzler* ------------------------------- Phone: +1-301-312-5145 LinkedIn <http://www.linkedin.com/in/fentonhorgchem/> On Mon, Jun 5, 2017 at 4:25 PM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hello Dr. Fenton Heirtzler, I agree it can be difficult to find specifics amongst a lot of text. I don’t know if this is what you meant, but from the “Minimize Structure” page: <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/minimize/ minimize.html>
"Energies (kJ/mol) are reported in the Reply Log. **Step numbers reported by MMTK are 2 greater than the actual numbers of minimization steps performed. The additional “steps” are not minimization steps but operations required to obtain gradient values and updated coordinates.**”
As I understand it there is no energy decomposition available directly from MMTK to Chimera, and thus only the total energy is reported. Total energies may be positive or negative depending on whether the positive interactions outweigh the negative interactions and conformational strain. As there is no decomposition, there is no way to tell how much of the total is from the strain vs. nonbonded interactions, or electrostatic vs. VDW interactions.
That said, my understanding is that simple molecular mechanics with atoms as nonpolarizable point charges is unlikely to provide an accurate representation of transition metal complexes, and Antechamber parametrization was not developed to handle such cases. This reply from several years ago somewhat addresses this issue, although the URL within it is no longer valid: <http://www.cgl.ucsf.edu/pipermail/chimera-users/2007-June/001665.html>
In short, you may need to use some other program to accurately model these situations. I hope this clarifies the situation, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jun 5, 2017, at 11:04 AM, Fenton Heirtzler < heirtzlerchempro@gmail.com> wrote:
Hello, I'm using Chimera to optimize the structures of several small-molecule transition metal complexes. The goal is to compare the steric energies of different diastereomers.
I've searched the local documentation on version 1.11.2 (Macintosh) for the term "Minimize structure" but found nothing which actually described the meaning,number format, reference points and units which are produced by the "Minimize Structure" command and appear in the "Reply log".
For example, the potential energy values which are returned can be either < 0 or > 0 (!!)
If a minimization is occurring, then the force field will describe those parameters - but the preceding values make no sense.
Some advice and instruction would be appreciated.
Thanks Dr. Fenton Heirtzler
participants (2)
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Elaine Meng -
Fenton Heirtzler