Hi Jason,
Thanks for the info. But is it possible for me to install AmberTools12 whilst still using Amber11?
I saw that your installation guide for installing AmberTools12 requires setting $AMBERHOME to 'amber12' directory.
However, I'm currently using Amber11 and my $AMBERHOME points to 'amber11'.
Will changing the $AMBERHOME path to 'amber12' directory still allow me to use Amber11?
I ask this because of my previous nightmare making Amber11 work on my Ubuntu machine :-)
Regards,
Adam
________________________________
From: Jason Swails <jason.swails.gmail.com>
To: AMBER Mailing List <amber.ambermd.org>
Sent: Thursday, June 7, 2012 10:31 AM
Subject: Re: [AMBER] Removing finite number of solvent particles from simulation box
On Wed, Jun 6, 2012 at 10:31 PM, Jason Swails <jason.swails.gmail.com>wrote:
>
>
> On Wed, Jun 6, 2012 at 9:12 PM, Adam Jion <adamjion.yahoo.com> wrote:
>
>> Hi!
>>
>> I need to remove a finite number of solvent particles from my simulation
>> box after every 200 ns.
>> Is it advisable to manually edit the .prmtop and .rst file?
>> Or is there a better way using tleap?
>>
>
> You can do it using parmed.py. See the "strip" command (xparmed.py will
> not let you write out a restart file, parmed.py will).
>
Note, parmed.py is part of AmberTools 12
>
> HTH,
> Jason
>
>
>>
>> Regards,
>> Adam
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Wed Jun 06 2012 - 22:00:03 PDT
