AMBER Archive (2004)

Subject: AMBER: parameter error for a ligand

From: Sivanesan Dakshanamurthy (sd233_at_georgetown.edu)
Date: Tue Oct 05 2004 - 11:59:54 CDT

Hi:

I am simulating a protein that contains a ligand. I have generated parameter for the ligand using 'antechamber'. Then I ran tleap for the complex (contain both protein & ligand). I have included the line that executes leap.in in order to get ligand top & crd files, here is the tleap and leap.in script which i have used:

TLEAP:
___________________________________________________
if ( ! ( $?AMBERHOME ) ) then
        echo "Error - must define environment variable AMBERHOME"
        exit(1)
endif
/usr/local/fbscapp/amber8/exe/tleap -s -f leap.in
$AMBERHOME/exe/teLeap -I$AMBERHOME/dat/leap/prep \
                        -I$AMBERHOME/dat/leap/lib \
                        -I$AMBERHOME/dat/leap/parm \
                        -I$AMBERHOME/dat/leap/cmd \
                        $*
____________________________________________________

leap.in:

___________________________________________________

source leaprc.gaff
mods = loadamberparams frcmod
loadamberprep LIG.prepin
saveamberparm HTW prmtop prmcrd
quit
_______________________________________

The following error occured while I ran tleap:

FATAL: Atom .R<HTW 553>.A<C10 1> does not have a type.
FATAL: Atom .R<HTW 553>.A<C9 2> does not have a type.
FATAL: Atom .R<HTW 553>.A<C8 3> does not have a type.
.............
.........
__________________________________

What may be the problem. How & where can I include the ligand topology & crd files, while run tleap for a protein complex.

Any help will deeply appreciated.

thanks
dak
    

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