Hello Fernaldo-- > I have a problem in generating XPLOR topology and parameter table for a small > molecule, 3'-5' cGAMP (cyclic guanine-adenosine monophosphate). > > I started out with crystal structure that contains this molecule, PDB ID: > 5cfm. > (It has residue name of "4BW"). I took this molecule and run xplo2d, and I got > the topology and parameter tables (attached). But I noticed that these tables > do > not include any proton, and I need the proton since I will be using them to > compute an NMR structure. >
Have you tried PRODRG? I believe that it does generate top/par files with protons. It may make some mistakes, though. For this molecule, you'll want to make certain to group the planar regions as rigid bodies. The dihedral term might be handled simply using 1-4 nonbonded interactions to avoid eclipsed conformations. Please contact me if you get stuck. best regards-- Charles _______________________________________________ Xplor-nih mailing list [email protected] https://dcb.cit.nih.gov/mailman/listinfo/xplor-nih
