AMBER Archive (2009)

Subject: [AMBER] How to run LEaP in a shell file?

From: SongLin (songlin_at_moon.ibp.ac.cn)
Date: Mon Dec 14 2009 - 01:10:00 CST

Dear professor,

I want to build PDB formatted glycan files using LEaP automatically, so
I create several shell files like this:

#!/bin/bash
cd ~/amber10/bin/
./tleap << !
source leaprc.GLYCAM_06
glycan=sequence{ROH}
glycan=sequence{glycan 3VA}
glycan=sequence{glycan 3LB}
glycan=sequence{glycan 0SA}
savepdb glycan glycan.pdb
quit
!

But when I run this file it returns:
*** Error: tl_getline(): not interactive, use stdio.

But it's ok when I run these commands line by line. Can you tell me how
to run LEaP automatically? (I can create LEaP command lines
automatically, but I can't run them automatically)

Thank you very much!

Yours Sincerely,
Lin Song

Center for Computational and Systems Biology,
Institute of Biophysics, CAS.
15 Datun Road, Chaoyang District
Beijing, 100101
P.R.China

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