![]() 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. By choosing these particular atoms, the inserted atom sits in an fcc site, which is. Reply: McGuire, Kelly: "Re: FFTK Water Interaction" to insert another atom in the average position of the three selected atoms.Next in thread: McGuire, Kelly: "Re: FFTK Water Interaction".Maybe in reply to: mariano spivak: "Re: FFTK Water Interaction".Previous message: Tom Bartl: "Re: 32bit memory problems on Mac OS".Next message: John Stone: "Re: 32bit memory problems on Mac OS".
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