AMBER Archive (2003)

Subject: Re: AMBER: saveamberparm

From: David A. Case (case_at_scripps.edu)
Date: Mon Nov 24 2003 - 19:32:22 CST

On Mon, Nov 24, 2003, Atchara Wijitkosoom wrote:
>
> I've tried using antechamber to generate topology and coordinate files
> for small molecules.
>
> > mods = loadamberparams frcmod
> Loading parameters: ./frcmod
> Reading force field mod type file (frcmod)
> > loadamberprep cit.prepi
> Loading Prep file: ./cit.prepi
> > saveamberparm CIT cit.top cit.crd
> saveAmberParm: Argument #1 is type String must be of type: [unit]
> usage: saveAmberParm <unit> <topologyfile> <coordfile>
>

You need to look in the cit.prepi file to see what name has been given to
the unit you created. This will be at the beginning of the 5th line of your
prepi file, and should be the same as the residue name in the pdb
file you gave to antechamber. It is this value that you must give as the
first argument to saveamberparm (where you have "CIT" above).

You can alway issue a "list" command in LEaP, after you do the loadAmberPrep
command, to see what unit's are defined. Unit names are case sensitive.

..good luck...dac 

-- 

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David A. Case                     |  e-mail:      case_at_scripps.edu
Dept. of Molecular Biology, TPC15 |  fax:          +1-858-784-8896
The Scripps Research Institute    |  phone:        +1-858-784-9768
10550 N. Torrey Pines Rd.         |  home page:                   
La Jolla CA 92037  USA            |    http://www.scripps.edu/case
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