AMBER Archive (2004)

Subject: Re: AMBER: paramitrization problem

From: lei jia (jial_at_broyde.nyu.edu)
Date: Tue Jun 08 2004 - 12:45:02 CDT

Hi Ross,

Just solved the problem. When I added new parameters in the parm99.dat file,I
put one more space line after the bond angle part. So perhaps this made the
program got confused. I followed your suggestions to create a frcmod file
containing new parameters. Loaded that in the leap. Then I had no problem to
add solvent and save the topology file!

Thank you very much for the help.

Best,

Lei Jia

Ross Walker wrote:

> Hi Lei,
>
> It sounds like there is something messed up with your .leaprc file. Would it
> be possible for you to post the contents of this file.
>
> The leaprc files in $AMBERHOME/dat/leap/cmd were created to load the correct
> library and parameter files for each of the different force field
> combinations. You can create your own .leaprc file to load whatever you want
> but what I tend to do is use the ones provided, e.g leaprc.ff99, and then
> manually load my own extra library files (using loadoff) and parameter files
> (using loadamberparams) once leap is running. This way it avoids any
> confusion that can arrise from editing the 'default' files.
>
> If you can send me a copy of your leaprc file and the pdb file from which
> you are trying to create the prmtop file I can take a look here and see if I
> can get it to work.
>
> All the best
> Ross
>
> /\
> \/
> |\oss Walker
>
> | Department of Molecular Biology TPC15 |
> | The Scripps Research Institute |
> | Tel:- +1 858 784 8889 | EMail:- ross_at_rosswalker.co.uk |
> | http://www.rosswalker.co.uk/ | PGP Key available on request |
>
> > -----Original Message-----
> > From: owner-amber_at_scripps.edu
> > [mailto:owner-amber_at_scripps.edu] On Behalf Of lei jia
> > Sent: 08 June 2004 08:00
> > To: amber_at_scripps.edu
> > Cc: ross_at_rosswalker.co.uk
> > Subject: RE: AMBER: paramitrization problem
> >
> > Dear Ross,
> >
> > Thank you for your suggestions. I think leap has loaded the parm file
> > since the lines at initiation are like these:
> >
> > Welcome to LEaP!
> > Sourcing leaprc: ./leaprc
> > Log file: ./leap.log
> > Loading parameters: ./parm99.dat
> > Loading library: /usr/local/etc/amber7/dat/leap/lib/all_nucleic94.lib
> > Loading library: /usr/local/etc/amber7/dat/leap/lib/all_amino94.lib
> > Loading library: /usr/local/etc/amber7/dat/leap/lib/all_aminoct94.lib
> > Loading library: /usr/local/etc/amber7/dat/leap/lib/all_aminont94.lib
> > Loading library: /usr/local/etc/amber7/dat/leap/lib/ions94.lib
> > Loading library: /usr/local/etc/amber7/dat/leap/lib/solvents.lib
> > >
> >
> > It sourced the leaprc file, which was modfied by adding new
> > atom types,
> > located in the current folder. I also found there is a
> > leaprc.ff99 file
> > in the amber folder. I didn't add new atom types to the leaprc.ff99
> > file. If I source the leaprc file instead of the leaprc.ff99
> > file, will
> > the leaprc.ff99 be read when I save the topology file? There are no
> > parameters missing when I checked unit. And I have no problem to add
> > ions. But I can't add water right and save the topology file.
> >
> > Thanks,
> >
> > Lei Jia
> >
> > --------------------------------------------------------------
> > ---------
> > The AMBER Mail Reflector
> > To post, send mail to amber_at_scripps.edu
> > To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu
> >

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