Hi Junaid,
If you want to use MCPB to deal with it, you need to have prep file of the system first (do RESP charge calculation using Gaussian, and
then use antechamber to generate the prep file, I recommend you to have the atom type in AMBER atom type) and then you can use
prep2xml to transfer the file into xml format, in which MCPB can recognize it. Then you can read the xml as lib file and do the normal
MCPB steps. It may contain a lot of trial and error process during the modeling.
Another way to deal with it is to define the bond, angle parameters by using a empirical way (and the charge still in RESP way),
in which you can check the former literatures, pick meaningful values and apply it in your system.
You can send me the structure file and I can help to look at it.
Best,
Pengfei
On Nov 19, 2014, at 2:20 AM, 杨川 <junaid.hust.edu.cn> wrote:
> Dear Amber Users
>
> I wan t to simulate the complex that contain Heme group using Amber14. We have got some problem in generating Heme parameters. The contributing parameters for Heme is for the Heme group attached to Histidine . But in our case the Heme is attached to Cysteine. We tried the MCPB function in Amber14 but the tutorial is not suitable for Heme, because in Heme the metal is not surrounded by amino acid residues.
> So i have attached the pdb file for Heme and associated to Cysteine. Could someone generate parameters or give some instructions on how to do it.
> Any help will be highly appreciated!!!
>
> Junaid
> <Heme_cysteine.pdb>_______________________________________________
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Received on Fri Nov 21 2014 - 07:30:02 PST
