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 - 16:30:02 PDT
