I just realised that you are posting to a mailing list that I thought I had closed down! Can you resend your email instead to [email protected]? This will have a greater reach.
By the way, right now my only thoughts are to check whether there's an IOP to convince G09 to write out more info. Or to do each of the scan manually using separate G09 calculations (if there's a way). Also, maybe put together a small example and attached the G09 logfile to your email? - Noel On Thu, 28 Feb 2019 at 11:49, Kenneth Irving <[email protected]> wrote: > Noel: thanks for the reply. In fact the problem is slightly more > complicated than the description I gave. > > What I'm actually trying to do is extract molecular coordinates from a > G09 surface scan. > > I know that G09 publishes the cartesian coordinates of the molecule at the > end of the output file and, as you say, I could use that info to get build > the internal coordinates. > > But the in which G09 does a scan calculation is this: > > For each point to be calculated, G09 publishes the initial cartesian > coordinates of the molecule. > > Having established a fixed distance bewteen two atoms (the scan > coordinate), G09 optimizes the rest of the coordinates and reports the > result... in internal coordinates!!! > > Then it changes the scan coordinate, reports the new initial coordinates > in cartesian (Input orientation), and proceeds to optimize the rest, > reportin the optimized result again in internal coordinates. The output > doesn't report optimized cartesian coordinates for each point, only > internal coordinates. > > It repeats this procedure for each of the scan values. > > For each point the optimized geometry is always reported in internal > coordinates, which are not exactly the ones I need to further prepare a > barrierless calculation using another program (multiwell). > > That is my problem: how can I use the internal coordinates information > given in G09 scan output to make useful (internal or cartesian) > coordinates I can use with multiwell. > > The way G09 is reporting the dihedral angle, is not exactly the one I need > to build the input for the other program. > > I reckon all the information is there: bond distances, bond angles and > dihedral angle. The problem is the way in which G09 particularly reports > the dihedral angle: 1,2,4,3 or 2,1,4,3 instead of 1,2,3,4 > > I havent' got a clue why G09 reports internal coodinates in this manner. > There must be a very good reason, but I haven't been able to find out. > > If I can transform the dihedral angle value to the original numbering, I > would be able to solve the problem. > > That's what I'm trying to find out. Or maybe I'm missing something quite > obvious. Any help is appreciated. > > best regards > > Kenneth > > On Thu, 28 Feb 2019, Noel O'Boyle wrote: > > > Are the atoms in the cartesian gaussian output in the same order as your > input atoms? If so, then you could use the library to calculate > > the dihedral angle yourself since you know which atom is which and their > cartesian coordinates. > > > > On Wed, 27 Feb 2019 at 18:59, Kenneth Irving via OpenBabel-scripting < > [email protected]> wrote: > > > > I have this simple molecule I'm studying: H2SCl > > > > The Gaussian 2009 (G09) input file is this: > > > > ---------- cut here ------------- > > #ub2plyp/6-31g(d,p) freq OPT > > > > adducto H2S--Cl > > > > 0 2 > > Cl > > S, 1, r1 > > H, 2, r2, 1, a1 > > H, 2, r3, 1, a2, 3, d1 > > Variables: > > r1=1.9 > > r2=1.0 > > r3=1.0 > > a1=120.0 > > a2=120.0 > > d1=120.0 > > > > ---------- cut here ------------- > > > > After running g09, I get these internal coordinate values in the > output > > > > ---------- cut here ------------- > > ! Name Definition Value Derivative Info. > > > > -------------------------------------------------------------------------------- > > ! R1 R(1,2) 2.7341 -DE/DX = 0.0 > > ! R2 R(2,3) 1.3401 -DE/DX = -0.0001 > > ! R3 R(2,4) 1.3401 -DE/DX = -0.0001 > > ! A1 A(1,2,3) 89.758 -DE/DX = 0.0 > > ! A2 A(1,2,4) 89.758 -DE/DX = 0.0 > > ! A3 A(3,2,4) 93.213 -DE/DX = 0.0 > > ! D1 D(1,2,4,3) -89.744 -DE/DX = 0.0 > > > > -------------------------------------------------------------------------------- > > ---------- cut here ------------- > > > > It's easy to see that G09 is not printing the same internal > coordinates > > I used in the input > > > > If I redefine the initial internal coordinates, putting sulphur as > > the first atom: > > > > ---------- cut here ------------- > > #ub2plyp/6-31g(d,p) freq OPT > > > > adducto H2S--Cl > > > > 0 2 > > S > > Cl, 1, r1 > > H, 1, r2, 2, a1 > > H, 1, r3, 2, a2, 3, d1 > > Variables: > > r1=2.9 > > r2=1.0 > > r3=1.0 > > a1=120.0 > > a2=120.0 > > d1=120.0 > > > > ---------- cut here ------------- > > > > ...I get these final internal coordinates: > > > > ---------- cut here ------------- > > ! Name Definition Value Derivative Info. > > > > -------------------------------------------------------------------------------- > > ! R1 R(1,2) 2.7349 -DE/DX = 0.0 > > ! R2 R(1,3) 1.3399 -DE/DX = 0.0 > > ! R3 R(1,4) 1.3399 -DE/DX = 0.0 > > ! A1 A(2,1,3) 89.7451 -DE/DX = 0.0 > > ! A2 A(2,1,4) 89.7451 -DE/DX = 0.0 > > ! A3 A(3,1,4) 93.2202 -DE/DX = 0.0 > > ! D1 D(2,1,4,3) -89.7303 -DE/DX = 0.0 > > > > ---------- cut here ------------- > > > > Distances and bond angles are no problem. The problem I'm having > is with > > the dihedral angle. > > > > In both cases the numbering in the dihedral angle is different > from the > > one I used in the input file. > > > > In the first case the dihedral angle in the input is numbered: > 4,2,1,3 but > > in the output I get: 1,2,4,3 > > > > In the second case the dihedral angle in the input numbered: > 4,1,2,3 but > > in the output I get: 2,1,4,3 > > > > For a different calculation I need to take these internal > coordinates > > results from G09 output and recreate the geometry in internal > coordinates > > but with the original numbering. As I said, distances and bond > angles are > > no problem. The problem is getting the original dihedral angle > from the > > internal coordinates data provided in the output. > > > > I was wondering whether I could do this with openbabel? > > > > I haven't been able to find a way that works for all cases: > depending on > > the atomic numbers, G09 displays different numbering of dihedral > angles. > > Apparently it lists atoms from the highest to lowest atomic number. > > > > Maybe there's a way I can use the internal coordinates in the > output to > > convert to cartesian coordinates and from there calculate the > internal > > coordinates with the original numbering. > > > > Maybe there's a simple way to convert dihedral angles based on > their > > numbering, but I haven't been able to come up with a solution, nor > have I > > found any literature on this topic. > > > > If someone could provide me with some guidance or has any idea, > I'd be > > very grateful. Thanks in advance. > > > > Best regards > > > > Kenneth > > > > > > > > > > _______________________________________________ > > OpenBabel-scripting mailing list > > [email protected] > > https://lists.sourceforge.net/lists/listinfo/openbabel-scripting > > > > > >
_______________________________________________ OpenBabel-scripting mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/openbabel-scripting
