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?
--Mickey Richards
University of Alberta
>
> --
> -------------------------
> Daniel R. Roe, PhD
> Lab Specialist
> Department of Medicinal Chemistry
> University of Utah
> 30 South 2000 East, Room 201
> Salt Lake City, UT 84112-5820
> http://home.chpc.utah.edu/~cheatham/
> (801) 587-9652
> (801) 585-9119 (Fax)
>
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Received on Tue Jul 24 2012 - 17:30:02 PDT
