On Tue, Jul 24, 2012 at 8:19 PM, Mickey Richards <mickey18385.gmail.com>wrote:
> Dan, thank you for your reply. Please see my responses below.
>
> On Tue, Jul 24, 2012 at 4:59 PM, Daniel Roe <daniel.r.roe.gmail.com>
> wrote:
> > Hi,
> >
> > Just to check, when you run Cygwin are you starting the X server?
>
> It's good to check. Yes, I am starting the X server as recommended in
> steps 4 and 5 (section 2) of this webpage:
> http://ambermd.org/mswindows.html .
> >
> >> 1. Is it only the AmberTools 1.5 version of xleap that will work for
> >> Windows/Cygwin?
> >
> > It is recommended that you upgrade to the latest version of AmberTools
> > (12, http://ambermd.org/#AmberTools) as there are many many
> > improvements and bug fixes over older versions; I can confirm that at
> > least AT12 xleap works for me using cygwin under Win7 x64.
>
> Thank you for that information!
> >
> >>
> >> 2. Can I use AmberTools 1.5 with Amber10 to set up simulations using
> >> PMEMD and explicit solvation?
> >
> > You can use Amber10 to run simulations and AmberTools to analyze them.
> > AmberTools12 can be installed alongside Amber10; see this post from J.
> > Swails (
> http://jswails.wikidot.com/installing-ambertools-12-and-older-amber)
> > for some helpful hints.
> > -Dan
>
> Thanks for the website recommendation. I had seen it earlier, but
> this sentence troubled me:
> "AmberTools 12 and Amber 11 are not directly compatible in that the
> sqm and pbsa libraries from AmberTools 12 will not work in sander from
> Amber 11 (the APIs have changed too much), so you will still need to
> download and install AmberTools 1.5 alongside Amber 11 (or AmberTools
> 1.2 alongside Amber 10, etc.)."
>
> If at all possible, I'd like to run xleap locally on my PC, rather
> than over the network - the graphical interface is slow over a
> network! I want to use xleap to generate the .crd and .top files that
> are appropriate for Amber 10. As I read your recommendation above,
> the version of xleap in AmberTools 1.5 should still create the
> necessary file for use in Amber 10. Is that correct?
>
Yes, but I suggest using AmberTools 12. The sentence above just says that
PBSA run in sander10 (or sander11) will *not* use the 'sqm' and 'pbsa'
libraries compiled with AmberTools 12. With those exceptions, AmberTools
12 will create files perfectly compatible with Amber 11 and earlier
(although note that Amber 10 does not support mixed 1-4 scaling which is
necessary to properly treat GLYCAM and Amber FF combinations).
HTH,
Jason
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Wed Jul 25 2012 - 07:00:03 PDT
