AMBER Archive (2008)

Subject: RE: AMBER: drawing repeated units

From: Ross Walker (
Date: Tue Jun 03 2008 - 18:49:54 CDT

Hi Taufi,

> Thank you Ross,
> It worked!
> Where can i learn to create a simple leaprc file. is it in any of the
> tutorials?

A leaprc file is just a text file containing the commands exactly as you
would enter them in leap. E.g. one could be:

source leaprc.ff99SB
loadamberparams my.frcmod
loadoff foo.lib
loadoff bar.lib
mol = sequence { FOO BAR FOO BAR }
saveamberparm mol prmtop inpcrd

Then you could just run this as:

tleap -s -f my.leaprc

and it would just run those commands and quit.

You can also do:

source my.leaprc

to read it from within an active leap session.

> i can also type mymol = sequence { FPRT REPU ... 50 100 150 and 200
> times.. ENDU } if writing a one -long- line script is too difficult.

You can't do that in leap unfortunately but you could either write a simple
perl or shell script that writes leaprc files for you - i.e. writes those
long lines for you. Or you could build some bigger units. I.e. build a unit
of 10 REPU's - so you would only have to put 10 of these units in to get a
100 repeat.

Good luck,

|\oss Walker

| Assistant Research Professor |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- |
| | PGP Key available on request |

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