Hello All-- > Thanks! I tried to use ACPYPE previously. That time there's > something wrong so it couldn't recognize my pdb file. Now it seems > OK. I just got the result. I like it not renaming my atoms, like > PRODRG. And its parameter file format is more similar to the file in > Xplor-NIH, thus easy to read. My ligand is a heme derived > molecule. As a quick check, I picked a pyrrole ring and sum its > interior angles equilibrium value. For a planar five-member ring, > such value should be equal to 540 degree. ACPYPE gives a result much > more than 540 degree, which is geometry impossible. I believe that's > because the parameter just comes from GAFF, which is not really > optimized for a specific case. While PRODRG just assign each > interior angle as 108 degree, although not so precise, at least the > ring will be kept planar.
Right. There are multiple problems with PRODRG output, so it's usually the beginning of the process. > So, I really like the writing of > ACPYPE. Unfortunately I still cannot use its result directly... > Sorry, I missed why you can't use the output directly. This is an ongoing pain,and I'd like to have a good general solution. It seems that if you have a PDB with good geometry and naming, this shouldn't be too difficult. Charles _______________________________________________ Xplor-nih mailing list [email protected] https://dcb.cit.nih.gov/mailman/listinfo/xplor-nih
