AMBER Archive (2003)

Subject: AMBER: Addles

From: Mark K. Dean (mkdean_at_essex.ac.uk)
Date: Wed Oct 08 2003 - 09:46:41 CDT

Hi, i am trying to use addles to setup a les region in Amber 7. initially
i am testing on a CYS residue defining the SG and HSG atoms as the les
region. Here is my input file to addles

~all filenames specified before action
~ specify input prmtop
file rprm name=(cys.prmtop) read
~ specify input cocrdinates
file rcvd name =(cys.prmcrd) read
~ specify LES prmtop
file wprm name= (LES.prmtop) wovr
~specify LES coordinates (velocities & box)
file wcrd name= (LES.crd) wovr
action
~do not scale masses of copied particles
omas
~copy cys side chain
spac numc=5 pick #prt 8 9 done
*EOD

The LES.prm* files are not created. Here is the addles.out file

add_les> ~ all filenames specified before action
add_les> ~
add_les> ~ specify input prmtop
add_les> ~ add_les> file rprm name=(cys.prmtop) read
  The following unit number was assigned 26
| New format PARM file being parsed.
| Version = 1.000 Date = 10/08/03 Time = 15:15:11
 Checking topology sizes against compiled limits
 Checking topology sizes against compiled limits
add_les> ~
add_les> ~ specify input cocrdinates
add_les> ~
add_les> file rcvd name =(cys.prmcrd) read
 getc

I would appreciate it if anyone could tell me what i am doing wrong.

Many thanks

Dr. Mark K. Dean
Royal Society - Wolfson Foundation Bio-Computing Lab
University of Essex
Wivenhoe Park
Colchester
Essex CO4 3SQ

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