What you're running into here (again) is the exact same issue from before,
going from the message- sander doesn't seem to have the NB type listed.
> I think I should change the atom type N5,N6 to NB(last mail I am wrong)
>
Changing your atom type back might work, but I've never done it before and
it still relies on whatever you rename it being already in mdread.f90- it
could also raise questions of how accurate the radii assigned to your atoms
will be. From what you've proposed, you could try looking for an atom with
a relatively similar radius already in mdread, ie how S+4 and P+5 could act
as similar substituents, and have that act as a stand in for MMPBSA. So in
this case, try to find another atom type in mdread.f90 that has a similar
radius to your metal atom.
Mind, I've never used MCPB or done what you're trying before, so I'm
talking from a general hypothetical perspective.
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.
>
I think this should be fine- as far as I know, ante-MMPBSA simply uses the
input topology as a source to create everything else without actually
modifying any terms present.
Also, if you're running on a cluster and don't have permission, you can
install AmberTools locally, edit the mdread.f90 and then try to have
someone with the adequate permission, ie an admin, replace the old mdread
with the edited one. I do realize that's not always doable, though, in
which case you'd be stuck with renaming the bad atom to a closely related
atom that's already there. I'd also suggest upgrading to AmberTools14
barring specific reasons, since your log looks like you're running
AmberTools12.
Best,
Kenneth
On Sunday, April 12, 2015, wjli <wenjuanli93.gmail.com> wrote:
> I think I should change the atom type N5,N6 to NB(last mail I am
> wrong).But there is still error:
>
> Error occured on rank 1.
> Exiting. All files have been retained.
> application called MPI_Abort(MPI_COMM_WORLD, 1) - process 6
> application called MPI_Abort(MPI_COMM_WORLD, 1) - process 1
> CalcError: /usr/local/amber12/bin/sander failed with prmtop com.top!
> Error occured on rank 7.
> Exiting. All files have been retained.
> application called MPI_Abort(MPI_COMM_WORLD, 1) - process 7
> bad atom type: NB
> CalcError: /usr/local/amber12/bin/sander failed with prmtop com.top!
> Error occured on rank 3.
> Exiting. All files have been retained.
> application called MPI_Abort(MPI_COMM_WORLD, 1) - process 3
> bad atom type: NB
> bad atom type: NB
> bad atom type: NB
> bad atom type: NB
>
>
> Did I think it too simple？I really need your help.
>
> ------------------ 原始邮件 ------------------
> 发件人: "wenjuanli93";<wenjuanli93.gmail.com>;
> 发送时间: 2015年4月12日(星期天) 下午2:09
> 收件人: "AMBER Mailing List"<amber.ambermd.org>; "amber"<
> amber.ambermd.org>;
>
> 主题: [AMBER] 回复：Re: Bad atom Type in MMPBSA.py
>
>
>
> 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
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sun Apr 12 2015 - 12:30:03 PDT
