When I needed to create some new atom types and parameters, I
ended up following the example of leaprc.ff99 in $AMBERHOME/dat/leap/cmd.
When I need it in xleap, I just type 'source leaprc.ppv' and it
loads in like the built-in force fields. The parm file (ppvmod.pcy)
and library files (*.off) are in dat/leap/parm and dat/leap/lib.
Here is my dat/leap/cmd/leaprc.ppv:
logFile leap.log
#
# leaprc for adding the atom types defined in ppvmod.pcy
# (This file was created by editing a copy of leaprc.ff99)
#
# load atom type hybridizations
#
addAtomTypes {
{ "SC" "C" "sp2" }
{ "TC" "C" "sp2" }
{ "CP" "C" "sp2" }
}
#
# Load the ppv frcmod parameters
#
parmppv = loadamberparams ppvmod.pcy
#
# Load t4r residue library
#
loadOff t4r_res.off
loadOff arms.off
#
Hope that helps - John
On Thu, 22 May 2003, Margaret Shun Cheung wrote:
> Dear All,
>
> I have created several new types of atoms using an arbituary force field.
>
> This is my command file, foo.cmd, for "xleap -s -f foo.cmd"
> =================================================
>
> clearVariables
> logFile foo.log
>
> addAtomTypes {
> { "AA" "C" "sp3" }
> { "AB" "C" "sp3" }
> { "AC" "C" "sp3" }
> { "AD" "C" "sp3" }
> { "AE" "C" "sp3" }
> { "AF" "C" "sp3" }
> { "AG" "C" "sp3" }
> { "AH" "C" "sp3" }
> { "AI" "C" "sp3" }
> }
> loadAmberPrep foo.in
> a = {R0 R1 R2
> }
>
> set a restype protein
> saveOff a ./foo.lib
>
> ===============================================
>
> then I load the parameter file
>
> > parmfoo = loadamberparams foo.dat
> > edit parmfoo
>
> I found that the types of made-up atoms are all gone,
> so I have to input them again by hand in the menu.
> However, whenever I tried to save the modification, xleap crashed
> with the following error message,
>
>
> XATRegisterShell: There are problems with WidgetCreatedTable
> !FATAL ERROR----------------------------------------
> !FATAL: In file [sysdepend.c], line 104
> !FATAL: Message: Illegal print string callback!!
> !ABORTING.
> Abort (core dumped)
>
>
> Can someone provide me a hint of how to fix it? Thank you very much.
>
>
> Sincerely,
>
> ----------------------------------------------------------------
> Margaret S. Cheung, Ph. D. | Tel: (301)405-7568
> Postdoctoral Fellow | Fax: (301)314-9404
> IPST Room 2116 | mscheung.ipst.umd.edu
> University of Maryland | http://glue.umd.edu/~mscheung
> College Park, MD 20742-2431 |
> ----------------------------------------------------------------
>
>
Received on Fri May 23 2003 - 03:53:01 PDT
