Dear Jason,
Thanks a lot. Now I have successfully generated topology and corresponding
coordinate file including ions. I appreciate your suggestion which was
really very helpful. I also appreciate Prof Case for---
http://archive.ambermd.org/201206/0313.html.
Regards
Kshatresh
On Sun, Apr 28, 2013 at 10:28 AM, Jason Swails <jason.swails.gmail.com>wrote:
> 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 Sun Apr 28 2013 - 00:30:03 PDT
