Dear all,

I have some question about the Charmm minimization in DS2.1. I minimized my protein with ligand and also sodium and chloride ions. I change name of sodium and chloride to SOD and CLA as exist in the topology of CHARMm, then fix the forcefield with this type of CHARMm. Indeed, I prefer to use Charmm27 but since there are many problems of ligands which cannot find a big set of parameters (if you have idea, please tell me, how to make it easy in case of ligand+protein with Charmm27?)

OK let's go back to my problem. When I defined SOD and CLA, there is no problem to fix forcefield. I continue for minimization. The result is OK, in Charmm.log...it was normal termination. Structure is OK...BUT!!! when I see in the intermediate directory. I found that my sodium ion was chaged to SULFUR in the mim.crd, molecule.crd and also molecule.psf files. But it's bizzare because in the output directory, the sodium is comming back in my protein.msv file!!!! So, how can I trust that my minimization using sodium , not sulfur!!!!!
Need someone has experience on this, give me some explanation, pleaseeee.....

Thank you for your kind help.