On Wed, Jul 25, 2012 at 7:39 AM, Jason Swails <jason.swails.gmail.com> wrote:
> 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
>
Thanks, Jason. That helps and makes perfect sense. I will install
AmberTools 12.
Also, thank you for the reminder that Amber 10 does not support mixed
1-4 scaling. It is good to have that information out there in
multiple places.
With best regards,
--Mickey Richards
University of Alberta
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Received on Wed Jul 25 2012 - 08:30:04 PDT
