AMBER Archive (2004)

Subject: Re: AMBER: parm94

From: bybaker_at_itsa.ucsf.edu
Date: Tue Aug 31 2004 - 17:15:04 CDT

('binary' encoding is not supported, stored as-is) Hello, Amber:

After loading the leaprc.ff94, I use the comman 'loadamberparams
parm94.dat' to load the parm94 force field which is downloaded from the
website (http://amber.scripps.edu/dbase.html). But it seems nothing
happen after the command, and I can't save .prmtop and .inpcrd files either.

The following is how I did with tleap:

guanine.3% $AMBERHOME/exe/tleap
-I: Adding /usr/local/amber7/dat/leap/prep to search path.
-I: Adding /usr/local/amber7/dat/leap/lib to search path.
-I: Adding /usr/local/amber7/dat/leap/parm to search path.
-I: Adding /usr/local/amber7/dat/leap/cmd to search path.

Welcome to LEaP!
(no leaprc in search path)
> source leaprc.ff94
----- Source: /usr/local/amber7/dat/leap/cmd/leaprc.ff94
----- Source of /usr/local/amber7/dat/leap/cmd/leaprc.ff94 done
Log file: ./leap.log
Loading parameters: ./parm94.dat
Loading library: /usr/local/amber7/dat/leap/lib/all_nucleic94.lib
Loading library: /usr/local/amber7/dat/leap/lib/all_amino94.lib
Loading library: /usr/local/amber7/dat/leap/lib/all_aminoct94.lib
Loading library: /usr/local/amber7/dat/leap/lib/all_aminont94.lib
Loading library: /usr/local/amber7/dat/leap/lib/ions94.lib
Loading library: /usr/local/amber7/dat/leap/lib/solvents.lib
> loadamberparams parm94.dat
Loading parameters: ./parm94.dat
> loadamberparams /home/socr/b/bybaker/parm94.dat
Loading parameters: /home/socr/b/bybaker/parm94.dat
> test1 = loadpdb N62-model1-2.pdb
Loading PDB file: ./N62-model1-2.pdb
  total atoms in file: 3375
> saveamberparm test test.prmtop test.inpcrd
saveAmberParm: Argument #1 is type String must be of type: [unit]
usage: saveAmberParm <unit> <topologyfile> <coordfile>

I don't undertand what is going on. Would you please give me some advices?

Thank you

Bo

On Tue, 31 Aug 2004 09:12:58 -0400 Asim Okur wrote:

> After loading any leaprc file (ff94 or 99) use the following command to
> load the desired force field
>
> loadamberparams filename
>
> Check the amber manual for more info,
>
> Cheers,
>
> Asim
> bybaker_at_itsa.ucsf.edu wrote:
>
> >Hello,
> >
> >I have another question related to the parm94 force filed. With tleap,
> >the program automatically recognize ff99 (or ff94) by the comands
> such as
> >'source leaprc.ff99 (or ff94), as the force fields are part of the
> >program. After downloading the modefiled force field files from the
> >website, how can I tell Amber to use it?
> >
> >Your help will be much appreciated.
> >
> >Bo
> >
> >
> >
> >On Mon, 30 Aug 2004 16:57:50 -0400 Carlos Simmerling wrote:
> >
> >
> >
> >>you can get just the force field files from
> >>http://amber.scripps.edu/dbase.html
> >>
> >>
> >>
> >
> >
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> >
>
> --
> Asim Okur
> Stony Brook University
> Chemisty Department
> Stony Brook, NY 11794-3400
> 631 - 632 1560
>
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