you can't use the "rcvb" command- this means to read in coordinates,
velociies and box size. You don't have those if it came from leap.
this is explained in detail in the manual, let us know if you have other
problems.
carlos
pang zhao wrote:
> 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 <http://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 <http://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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Received on Wed May 17 2006 - 06:07:09 PDT
