Dear Kenneth, Thanks for your reply.I am trying other ways because I dont have permission to do that. After the md production done,I modify the .top file (change the N5,N6 back to ND1 atom) and use this file to run ante-MMPBSA.py.I dont know if it's right to do that. wjli
------------------ ÔʼÓʼþ ------------------
·¢¼þÈË: "Kenneth Huang";
·¢ËÍʱ¼ä: 2015Äê4ÔÂ12ÈÕ(ÐÇÆÚÌì) Á賿2:17
ÊÕ¼þÈË: "AMBER Mailing List";
Ö÷Ìâ: Re: [AMBER] Bad atom Type in MMPBSA.py
Hi,
MMPBSA is just saying that it doesn't have the appropriate entry to assign
radii for your new atom types- you'll have to edit the mdread.f90 file in
$AMBERHOME/AmberTools/src/sander with your new atom types. Search the file
for 'bad atom type', and there should be an entry for it right below Mg-
you can add in an entry with the name of your molecules, and the
appropriate information there.
Note, that after you modify mdread, you'll need to recompile AmberTools for
it to take effect.
Best,
Kenneth
On Fri, Apr 10, 2015 at 10:35 PM, wjli <wenjuanli93.gmail.com> wrote:
> Dear Amber members,
>
> I use MCPB to model metal ions.For the coordinated atom ,I rename it to
> N5,N6(just like the Tutorial done).But MMPBSA.py can't recognize the
> atoms.What should I do for the modification?
>
> Look forward to your reply!
> Best wishes.
> wjli‍
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Received on Sat Apr 11 2015 - 23:30:02 PDT
