![]() This same procedure holds for scanning any other kind of geometrical variable. for our hypothetical calculation we could write the second line as 2 1 5 8 S 4 45.0 with which the dihedral angle would be scanned from 0.0 degrees to 180.0 degrees in 45.0 degrees steps) In this way, the second step of our hypothetical calculation would look like the molecule on figure 3, and the convergence criteria would be reached much faster. The first line will make all other dihedral angles around the C2-C3 bond to behave in the same way as D, steps is the number of increments in the variable to be performed from the starting geometry and increment is the step size to be taken in the variable (Note this values are always in integer format so a decimal point is always to be used! e.g. Hence, before defining the variable to be scanned we must select carefully, through the use of wildcards all other variables associated with it. This would result in an unefficient method for computing the desired barrier. Since the value of D is kept constant until convergence then the algorithm (provided a decent level of theory is indicated when it comes to molecules more interesting than ethane) will increase the values of dihedral angles D and D until reaching the convergence criteria at a regular structure. If we define the dihedral angle 2-1-5-8 (fig.1) to be scanned from 180.0 deg to 0.0 by 45.0 degrees increments then the second step of the scan would look distorted like the molecule on figure 2. Lets say we want to calculate the energy barrier associated with the rotation of a dihedral angle on ethane. Therefore the use of wildcards is compulsory and it is illustrated below. The worst case scenario would consist of the molecule’s complete distortion from any physically achievable structure, making the calculation end with an error or by providing meaningless results. ![]() This means that functional groups can be destroyed on each step and in the best case scenario the optimization algorithm will put it back together again at, of course, some unnecessary computational cost. A common mistake is to define the variable to scan without taking into consideration all the other variables which depend from the first. Using internal coordinates becomes compulsory and a well-defined Z-Matrix is preferable. ".fftk_. use of Internal Redundant coordinates (through the Opt=ModRedundant option) must not be overlooked! This option performes a geometry optimization at each step while maintaining the scanned variable constant, which is referred to as a Relaxed Potential Energy Surface (PES) Scan. "::ForceFieldToolKit::GenZMatrix::genZmatrix" (procedure "::ForceFieldToolKit::GenZMatrix::genZmatrix" line 89) "::ForceFieldToolKit::GenZMatrix::writeZmat $acceptorAtom acceptor $Gnames $outfile" ![]() (procedure "::ForceFieldToolKit::GenZMatrix::writeZmat" line 167) The error says:Ītomselect: cannot parse selection text: index I believe the error is talking about the copper atom. What is the workaround at this FFTK step for new atoms that need to be Acceptor atoms? I am using VMD 1.9.4a12. It correctly writes Gaussian Input Files for my other Acceptor and Donor atoms without problems. The Gaussian Input File, CAI-ACC-Cu.gau, is blank. FFTK identifies my copper atom as an Acceptor atom, but can't write a Gaussian Input File for it. I have defined my own parameters based on copper CHARMM parameters from literature. I have atom type that is not in the CGENFF parameters, it is copper. ![]() I am running into an error in the water interaction FFTK step. ![]() On Thu, at 12:30 AM McGuire, Kelly > wrote: If you still have problems, you could send me the files (psf, pdb, par/str) and I could take a look. Subject: Re: vmd-l: FFTK Water Interactionīased on the error you report, the issue you experience is related to the bonds defined for the copper atoms (if any) in the psf file.įftk is trying to generate a zmatrix around the copper to orient the corresponding water molecules, but it does not found any bonds to set a frame of reference for the zmatrix.Ĭan you check the psf for bonds with the copper atom? For example, if this is a coordination complex, you might need to add explicitly the bonds to the copper atom. Out of curiosity, are nonbonded atoms (no specific scenario) always a problem with FFTK?ĭepartment of Physiology and Developmental Biology Explicit bonds are required and need to specified in the PSF.
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