4/4/2014

AMBER 12 AmberTools 13

Tags amber, md
Edited Feb 7, 2014 6:50 PM by Frank Beierlein

AMBER 12 AmberTools 13
< Software used at the CCC < AMBER overview -----------------------(This first section is still experimental - please tell me if anything doesn't work.)

To use interactive tools like xleap, ptraj, antechamber (AmberTools 13) etc. on machines like ccc138:
Type the following command (should be found automatically, as it is in /ccc/SOFT/bin) to get the path and AMBERHOME set correctly: u s e A m b e r 1 2 A T 1 3 . c s h

To submit sander, pmemd etc. jobs on cccserver:

A submit-script for the ccdh cluster should be found automatically, as it is in /ccc/SOFT/bin. To use it and to get information how to use it, type: a m b e r 1 2 c c d h

----------------ALTERNATIVE, for geeks only:

Do it the the old-fashioned way. Amend your .login or your .cshrc first: s e tp a t h=($ p a t h/ c c c / S O F T / a m b e r / a m b e r 1 2 _ A T 1 3 _ g n u / b i n ) s e t e n vA M B E R H O M E/ c c c / S O F T / a m b e r / a m b e r 1 2 _ A T 1 3 _ g n u Then open a new shell or: s o u r c e. c s h r c This should make tleap, xleap, ptraj, antechamber etc. available. (Attention: Pressed Numlock will cause trouble for xleap!) If you want to use Amber in parallel, e.g. on 4 CPU cores, you can also add (this is only needed to do the tests) s e t e n vD O _ P A R A L L E L' / u s r / l i b 6 4 / m p i / g c c / o p e n m p i / b i n / m p i r u nn p4 '
http://ccca140/groups/ccc/wiki/80d19/AMBER_12_AmberTools_13.html 1/2

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AMBER 12 AmberTools 13

You can then run sander.MPI or pmemd.MPI interactively on e.g. 4 processors using / u s r / l i b 6 4 / m p i / g c c / o p e n m p i / b i n / m p i r u nn p4s a n d e r . M P I . . . or / u s r / l i b 6 4 / m p i / g c c / o p e n m p i / b i n / m p i r u nn p4p m e m d . M P I. . . As far as I know, nobody has bothered yet to compile Amber12 using IFORT.

To run sander/pmemd interactively and to use interactive tools like xleap, ptraj, antechamber (AmberTools 13) etc. on eamon[1-3] (if you are sitting in EAM):
You need to amend your .cshrc or your .login first: s e tp a t h=($ p a t h/ h o m e / b e i e r l / s o f t w a r e / a m b e r 1 2 / b i n) s e t e n vA M B E R H O M E/ h o m e / b e i e r l / s o f t w a r e / a m b e r 1 2

If you want to use Amber in parallel, e.g. on 4 CPU cores, you can also add (this is only needed to do the tests) s e t e n vD O _ P A R A L L E L' / u s r / b i n / m p i r u nn p8 '

You can then run sander.MPI or pmemd.MPI interactively on e.g. 4 processors using / u s r / b i n / m p i r u nn p4s a n d e r . M P I. . . or / u s r / b i n / m p i r u nn p4p m e m d . M P I. . .

http://ccca140/groups/ccc/wiki/80d19/AMBER_12_AmberTools_13.html

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