AMBER Archive (2003)

Subject: Re: AMBER: Addles

From: xiaolin cheng (cheng_at_ilion.bio.sunysb.edu)
Date: Wed Oct 08 2003 - 10:56:18 CDT

Hi,

Your LES output file shows ADDLES stopped when it was reading the coordinate
file.
You can try "rcrd" option instead of "rcvd" since "rcvd" reads in coordinate
+ velocity.

Best

xiaolin
----- Original Message -----
From: "Mark K. Dean" <mkdean_at_essex.ac.uk>
To: <amber_at_scripps.edu>
Sent: Wednesday, October 08, 2003 10:46 AM
Subject: AMBER: Addles

>
> 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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