AMBER Archive (2004)

Subject: RE: AMBER: paramitrization problem

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Tue Jun 08 2004 - 12:31:10 CDT

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
>
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