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How to set up heme+protein complex for CpHMD use?
#34264 08/11/14 05:28 PM
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Hi all,

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.

Best


Zhi (Shane) Yue
Department of Chemistry
University of Chicago
Re: How to set up heme+protein complex for CpHMD use?
shane yue #34265 08/11/14 06:58 PM
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rmv Offline
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If the bond to Fe depends on the His protonation state, it's not clear how this should be handled, or if PHMD is the right method.

I think this is an issue you should probably discuss with your research adviser, senior members of your research group, or other local experts. If that doesn't help, you may need to contact PHMD developers directly for guidance.


Rick Venable
computational chemist

Re: How to set up heme+protein complex for CpHMD use?
rmv #34267 08/11/14 09:31 PM
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Hi Rick,

Thanks for your comments. I'll talk to my adviser. I have another question. When do people normally use "FHEM" patch? I just learnt that "FHEM" patch introduces a free heme. Thanks.

Best


Zhi (Shane) Yue
Department of Chemistry
University of Chicago
Re: How to set up heme+protein complex for CpHMD use?
shane yue #34271 08/11/14 10:15 PM
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rmv Offline
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The FHEM patch removes a couple unwanted angles involving heme N atoms and the Fe atom that were added by AUTOgenerate, and nothing else. No linkage to a His residue or a gas molecule is assumed or defined. It is typically used as an alternative to PHEM, which creates the bond between His NE2 and FE, and also removes the unwanted angles.


Rick Venable
computational chemist


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