Hi Yuan,
You can use the “combine” command to combine two structures together using LEaP to create the complex: see Page 220 of the AmberTools17 manual: http://ambermd.org/doc12/Amber17.pdf <http://ambermd.org/doc12/Amber17.pdf>.
Kind egards,
Pengfei
> On Dec 12, 2017, at 4:14 AM, MinYuan <minyuan.mail.ustc.edu.cn> wrote:
>
> Hi,
>
> I have inpcrd and prmtop files of an enzyme and a small molecule, respectively.
> Both are generated by MCPB.py.
> ( metal ions contained in enzyme as well as small molecule.)
>
> But how to generate coordinates and topology files of the complex (enzyme+small molecule).
>
> Is there any way to combine the two sets of files together?
> Or need I use MCPB.py based on the initial complex...The question is can MCPB.py deal with two metal-like sites simultaneously?
>
> Looking forward to hear you help.
>
> Best wishes
> Yuan Min
>
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Received on Wed Dec 13 2017 - 09:00:02 PST
