Hello,
Internally in SEBOMD, there is a table that converts any atom type into an
atomic number. I guess this is where the problem is (SPC/Fw atom types may
not have been included).
Can you send me your topology and coordinate file please so that I can look
into it and check if I can provide a patch?
Thanks,
Gerald.
On Tue, Jul 27, 2021 at 4:03 AM Daniel Konstantinovsky <
daniel.konstantinovsky.yale.edu> wrote:
> Hi everyone,
>
> I am trying to do an AM1 minimization and simulation of a small water box
> using the SEBOMD plug-in and a topology I made for SPC/Fw simulation of the
> same box. AMBER throws this error:
>
> *ERROR: NO PARAMETER FOR ATOM 1 (ATOMIC NUMBER = 8)*
>
> It seems something is wrong with the topology. This topology works for
> classical SPC/Fw runs. How can I fix this?
>
> My input file is
>
> &cntrl
> imin=1,
> maxcyc=5000,
> ncyc=2500,
> nmropt=0,
> ntb=1,
> cut=5,
> ntwx=500,
> ioutfm=1,
> iwrap=1,
> ifqnt=1,
> /
> &qmmm
> qm_theory='SEBOMD',
> /
> &sebomd
> hamiltonian='AM1',
> charge=0,
> longrange=1, ! PME
> /
>
> Thank you!
> Dan Konstantinovsky
> _______________________________________________
> 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 Mon Jul 26 2021 - 17:00:02 PDT
