Re: [AMBER] error with chamber

From: Crowley, Michael <Michael.Crowley.nrel.gov>
Date: Tue, 3 Apr 2012 14:18:00 -0600

You probably have more than one .prm file in your directory, check that,
but better would be to not use the * and just spell out the file.
Cheers,
Mike

-- 
Michael F. Crowley, Ph.D.
Principal Scientist, Biomolecular Sciences Division
National Renewable Energy Laboratory
1617 Cole Blvd.
Golden, CO 80401
303-384-6345 office
303-887-0149 cell
On 4/3/12 2:15 PM, "Albert" <mailmd2011.gmail.com> wrote:
>Hello:
>
>    I've built a MD system from CHARMM-GUI and I would like to convert
>it to Amber system by chamber. Since there are many topologies involved
>for this system, and I am trying to run chamber by command:
>
>  chamber -cmap -top toppar/*.top -param *.prm -psf
>step5_assembly.xplor_ext.psf -crd step5_assembly.pdb -p amber.prmtop
>-inpcrd amber.inpcrd -box 90 90 120
>
>but chamber said:
>       Error unknown flag: par_all22_prot.prm
>
>probably my syntax is not correct and chamber don't know how to deal
>with multiple topology and parameter files? Does any body have any
>suggestions?
>
>thank you very much
>
>best
>
>Albert
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Received on Tue Apr 03 2012 - 13:30:03 PDT