Hello!
I am building the topology files using sleap for my complex, receptor and
ligand. But I do not any any charges for ligand in the top file.
The leap script is as follows:
source leaprc.ff99SB
source leaprc.gaff
loadamberparams gaff.dat
loadAmberParams lig.frcmod
loadamberprep lig.prepi
LIG = loadmol2 lig.mol2
receptor = loadPDB receptor.pdb
complex = combine {receptor LIG}
set default PBRadii mbondi2
saveAmberParm LIG lig.top lig.crd
saveAmberParm receptor rec.top rec.crd
saveAmberParm complex com.top com.crd
savemol2 complex complex.mol2
savemol2 receptor receptor.mol2
solvateOct complex TIP3PBOX 15.0
addions complex Na+ 0.0
saveAmberParm complex com_solvated.top com_solvated.crd
savemol2 complex com_solvated.mol2
quit
lig.top
%VERSION VERSION_STAMP = V0001.000 DATE = 10/05/10 20:18:35
%FLAG TITLE
%FORMAT(20a4)
lig.pdb
%FLAG POINTERS
%FORMAT(10I8)
42 10 18 26 38 37 75 52
0 0
217 1 26 37 52 19 33 13
12 0
0 0 0 0 0 0 0 0
42 0
0
%FLAG ATOM_NAME
%FORMAT(20a4)
C1 H1 H2 H3 S1 O1 O2 C2 C3 H4 C4 H5 C5 H6 C6 H7 C7 C8 O3
N1
H8 C9 H9 H10 C10 H11 H12 C11 C12 H13 N2 H14 C13 C14 C15 H15 C16 H16 C17
H17
C18 H18
%FLAG CHARGE
%FORMAT(5E16.8)
0.00000000E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00
0.00000000E+00
0.00000000E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00
0.00000000E+00
0.00000000E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00
0.00000000E+00
0.00000000E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00
0.00000000E+00
0.00000000E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00
0.00000000E+00
0.00000000E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00
0.00000000E+00
0.00000000E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00
0.00000000E+00
0.00000000E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00
0.00000000E+00
0.00000000E+00 0.00000000E+00
lig.prepi file
0 0 2
This is a remark line
molecule.res
ABC INT 0
CORRECT OMIT DU BEG
0.0000
1 DUMM DU M 0 -1 -2 0.000 .0 .0 .00000
2 DUMM DU M 1 0 -1 1.449 .0 .0 .00000
3 DUMM DU M 2 1 0 1.522 111.1 .0 .00000
4 C3 ca M 3 2 1 1.540 111.208 180.000 -0.084409
5 H4 ha E 4 3 2 1.074 82.562 -145.176 0.159598
6 C2 ca M 4 3 2 1.384 156.318 40.109 -0.031192
7 S1 s6 3 6 4 3 1.774 119.554 176.486 1.092920
8 C1 c3 3 7 6 4 1.776 104.322 84.887 -0.551183
9 H1 h1 E 8 7 6 1.081 109.480 -61.407 0.184348
10 H2 h1 E 8 7 6 1.081 109.516 60.583 0.184348
11 H3 h1 E 8 7 6 1.082 106.522 179.650 0.184348
12 O1 o E 7 6 4 1.437 107.673 -161.219 -0.583711
13 O2 o E 7 6 4 1.435 108.390 -29.326 -0.583711
14 C4 ca M 6 4 3 1.388 121.273 -2.994 -0.106108
15 H5 ha E 14 6 4 1.073 119.827 177.891 0.161836
16 C5 ca M 14 6 4 1.383 119.089 -0.546 -0.186145
17 H6 ha E 16 14 6 1.075 120.032 178.503 0.159350
......
Could you please provide some suggestions.
Thanks
AD
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Received on Tue Oct 05 2010 - 19:00:03 PDT
