On Thu, 2014-05-15 at 13:33 +0400, James Starlight wrote:
> Thanks Dan,
>
> using -at amber have reduced output only to two errors
>
> Checking for angle parameters.
> Could not find angle parameter: C - N - CM
> Could not find angle parameter: HA - C - N
> There are missing parameters.
>
> I dont know exactly to what CM and HA atoms can be changed in accordance
> to standard a.a names in case of my chromophore so I'll try to add its
> manually
Don't change the atom names manually unless you know that antechamber
misassigned certain types.
Instead, just create a frcmod file (or modify your existing frcmod file
if you got one from parmchk) to add C-N-CM and HA-C-N angle terms. You
can look through the $AMBERHOME/dat/leap/parm/parm10.dat file for
similar terms to use.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Thu May 15 2014 - 04:30:02 PDT
