Hope you've just had a fantastic weekend! I'm trying to set up a heme-protein system. I have several questions wrt how to build the system.
1. Based on my previous experience on simulating protein complex, I think I should extract protein and heme from the original PDB into separate files. Then generate PSF individually. Finally combine the two. I'm not sure whether this is the right strategy. I know normally a heme patch (PHEM or FHEM) should be used and the histidine coordinated with heme should be HSD. But seems that does not work for me (see below).
2. As I'm gonna use CpHMD, HSP will be used for all histidines to titrate them. Thus I think it is better to leave heme uncoordianted. In other words, I think I should use HEME rather than PHEM or FHEM. But I'm not sure whether this is right or doable. If not, then how can I deal with it?
Hope someone can help me. Thanks in advance.