Hello 陈家良-- > > My protein has a Mg2+ in the pdb file, but the psf file generate by "pdb2psf" > command did not contain the Mg2+ information.
In the PDB file, if you change the HETATM literal for to "ATOM ", such that the beginning of the associated line reads ATOM XXXX MG+2 MG2 pdb2psf should produce a working PSF file, and protocol.initCoords should read the coordinates in a script, if preceded by protocol.initStruct. Alternately, you could simply use protocol.loadPDB, and then there would be no PSF file required. I tested this with Xplor-NIH version 2.47. Manually editing PSF files is error-prone and not recommended. best regards-- Charles _______________________________________________ Xplor-nih mailing list [email protected] https://dcb.cit.nih.gov/mailman/listinfo/xplor-nih
