Hi Ming,
I had a similar issue recently with Fe not being recognized by MMGBSA. Please check out the relevant previous ListServe posts given below. I actually wish I found the first one by Dr. Case when I was dealing with this issue.
http://archive.ambermd.org/201606/0311.html <
http://archive.ambermd.org/201606/0311.html>
http://archive.ambermd.org/201303/0230.html <
http://archive.ambermd.org/201303/0230.html>
As indicated in the second of these posts, you can see what atoms are defined for MMGBSA by inspecting the mdread2.f90 source file in the AmberTools directory. You can also add parameters there, assuming you've obtained them in some respectable way. Note that the second post speaks of a “mdread” file, but since then, my understanding is that the name changed to mdread2.
I hope these comments help.
Best,
Matthew
> On Sep 1, 2021, at 8:05 PM, Ming Tang <m21.tang.qut.edu.au> wrote:
>
> *Message sent from a system outside of UConn.*
>
>
> Dear developers,
>
> I came across the below problem when using mmpbsa.py in AmberTools19
> bad atom type: i
>
> Does AmberTools21 handle "I" atom?
>
> Thanks,
> Ming
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Received on Wed Sep 01 2021 - 17:30:02 PDT
