On Sat, Apr 27, 2013 at 5:28 PM, Kshatresh Dutta Dubey
<kshatresh.gmail.com>wrote:
> Dear Ross
>
> Thanks for your quick reply. I went through the leap.log file and found
> that ions08.lib was already loaded. In previous versions of Ambertools, I
> never used separate definition of parameters of Na and Cl during addIons.
> Then why is it so? Furthermore, I am unable to find out the solution in
> manual i.e. Ambertool12, ( I went through and found nothing except addIons
> and addIon2). Please, suggest me in some more details as I am unable to
> find useful information regarding this error in manual and tutorial.
>
The solution is actually in the manual. Look at Chapter 2, Section 9 in
the AmberTools manual. Prior to AmberTools 1.5 (I think), the default ion
parameters (the Åqvist et al. parameters, IIRC) were removed from the
various force fields. This was done because recent work has shown that the
'best' ion parameters to use depends strongly on the water model you wish
to include in your simulation.
Therefore, there is a different frcmod file for each solvent model (again,
listed in section 2.9). You need to deliberately choose the parameters for
the solvent model you want to use (that way, users know they have to be
deliberate about the parameters they run with, reducing the likelihood of
making a mistake.
HTH,
Jason
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Sat Apr 27 2013 - 22:30:02 PDT
