Ok, thanks for your reply. Because I am new to Constant pH MD simulation,
so I still have a question. The Arg residue is not titratable in Amber with
constant pH method, so, why is that ?
2014-10-16 16:11 GMT-07:00 Jason Swails <jason.swails.gmail.com>:
> On Thu, Oct 16, 2014 at 6:07 PM, jinfeng liu <jinfengliu1119.gmail.com>
> wrote:
>
> > Hi all,
> >
> > I am trying to run constant pH MD with amber14. But I am getting some
> error
> > messages in tleap when I load the libraries for constph. The error
> messages
> > are as follows, which are highlighted:
> >
> > ----- Source: /home/jinfeng/amber14/dat/leap/cmd/leaprc.constph
> > ----- Source of /home/jinfeng/amber14/dat/leap/cmd/leaprc.constph done
> > ----- Source: /home/jinfeng/amber14/dat/leap/cmd/oldff/leaprc.ff10
> > ----- Source of /home/jinfeng/amber14/dat/leap/cmd/oldff/leaprc.ff10 done
> > Log file: ./leap.log
> > Loading parameters: /home/jinfeng/amber14/dat/leap/parm/parm10.dat
> > Reading title:
> > PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA
> > Loading library: /home/jinfeng/amber14/dat/leap/lib/amino10.lib
> > Loading library: /home/jinfeng/amber14/dat/leap/lib/aminoct10.lib
> > Loading library: /home/jinfeng/amber14/dat/leap/lib/aminont10.lib
> >
> > *Could not open file phosphoaa10.lib: not foundCould not open database:
> > phosphoaa10.lib*
> >
>
> Hmmm... it looks like this file was deleted from the distribution last
> March (2013). It was replaced with "updated" versions of the
> phosphorylated amino acids in separate lib files.
>
> The problem is that constant pH still relies on an "old" force field
> (ff99SB, which is equivalent to ff10 for proteins). I've heard talk of
> people *planning* to update the reference energies to support ff14SB
> instead, but this hasn't happened yet.
>
> As long as you don't plan on using phosphorylated amino acids in your
> constant pH simulations, you can safely ignore this.
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
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Received on Thu Oct 16 2014 - 17:30:02 PDT
