Dear AMBER:
I was trying to siumulate protein with the cognate
ligand.
I tried to assign parameters for ligand separately.
Hence, I ran the following script:
/usr/local/fbscapp/amber8/exe/antechamber -i LIG.pdb
-fi pdb -o LIG.prepin \
-fo prepi -c bcc -nc -0 || goto error
/usr/local/fbscapp/amber8/exe/parmchk -i LIG.prepin -f
prepi -o frcmod || goto error
/usr/local/fbscapp/amber8/exe/tleap -s -f leap.in >
leap.out
/usr/local/fbscapp/amber8/test/dacdif -t 0
LIG.prepin.save LIG.prepin
/usr/local/fbscapp/amber8/test/dacdif frcmod.save
frcmod
/usr/local/fbscapp/amber8/test/dacdif -t 0 prmtop.save
prmtop
/bin/rm -f ANTE* ATOMTYPE.INF BCCTYPE.INF FOR*
NEWPDB.PDB PREP.INF \
prmcrd divcon.in divcon.rst divcon.dmx
exit(0)
error:
echo " ${0}: Program error"
exit(1)
The OUTPUT Look like below:
Total number of electrons: 208; net charge: 0
Running: /usr/local/fbscapp/amber8/exe/divcon
Cannot open LIG.prepin.save: No such file or directory
diffing LIG.prepin.save with LIG.prepin
possible FAILURE: check LIG.prepin.dif
==============================================================
diffing frcmod.save with frcmod
possible FAILURE: check frcmod.dif
==============================================================
Cannot open prmtop: No such file or directory
diffing prmtop.save with prmtop
possible FAILURE: check prmtop.dif
==============================================================
could you help me to the following:
1. What was the problem in my input.
2. after having the ligand parameters assigned , I
need to add the ligand coordinates to its receptor
file, so that complex will formed.
At this point, how can I include the ligand parameters
in the LEAPRC file.
I would appreciate your reply,
Thanks
siva
D.Sivanesan, Ph.D.
Dept. of Oncology,
Lombardi Cancer Center (NCI Comprehensive Cancer Center),
Georgetown University, DC 20057
Phone: 202-687-6338
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Received on Fri Jul 02 2004 - 19:53:01 PDT
