AMBER Archive (2006)

Subject: AMBER: fail to execute addles

From: pang zhao (zhao.pang_at_gmail.com)
Date: Mon May 15 2006 - 06:59:10 CDT

Dear All,

I am new to LES. When I execute addles according to the manual9 with amber9,
but fail at every time.

My input les.in:
~
file rprm name=(a.top) read
file rcvb name=(a.crd) read
file wprm name=(les.top) wovr
file wcrd name=(les.crd) wovr
action
~
omas
~

spac numc=3 pick #prt 343 343 done
*EOD

I want to just copy the ligand 343

For the a.top, a.crd, the a.pdb has 342 residues and one ligand 343, it was
solved with xleap with about 6000 TIP3P water. This a.crd,a, a.top are
normal and I can use it to run sander.

when I execute:
addles < les.in > les.out
The content of the subsquently obtained les.out :

AMBER9 Module: addles
set up Locally Enhanced Sampling topology
add_les> ~
add_les> file rprm name=(a.top) read
The following unit number was assigned 26
| New format PARM file being parsed.
| Version = 1.000 Date = 03/04/05 Time = 11:07:26
Checking topology sizes against compiled limits
Checking topology sizes against compiled limits
add_les> file rcvb name=(a.crd) read
The following unit number was assigned 27
Coords, velocities and box from unit 27
Reading coordinates from input file
Reading velocities from input file
crd file end

But I do not get the les.top,les.crd.
What is the problem? Lookinf forward to any suggestions.

Best wishes

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