Dear Charles,<br/><br/>Replacement of "HETAM" with "ATOM" in PDB file indeed generated the psf file containing Mg2+ informnation. But the script reported another error "PDBTool:read: atom not found in structure: " by protocol.initCoords reading the coordinates (all atoms in the pdb file were not found). It seems that the psf file was still not working.<br/>The protocol.loadPDB worked well. But when I input coordinates of GDP ligand and some axis by protocol.initCoords (psf file also loaded by protocol.initStruct), an error is "SystemError: xplor-nih error: Error: named selection with name pseudo contains an inconsistent number of atoms.". I also tried loaded coordinates of GDP and axis by protocol.loadPDB, it also did not work. <br/>My program version was 2.35, is it ok?<br/>I would really appreciate your help.<br/><br/>Best regards<br/>Jia-Liang Chen<br/>Nankai University, China 在 2017-12-30 00:16:05，Charles Schwieters <[email protected]> 写道： > >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
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