Hello everyone:
Recently I want to run the trajectory of cytochrome c553(
PDB: 1B7V) which has a heme.In order to prepare the parameters of this
system,I extract the heme and the part of HIS and two CYS(In HIS the epsilon
N atom form bond with FE,and In two CYS,the S atom form bond with FE. )from
c533 system ,So obtain the system[Fe(porphyrin)(imidazole)(S(CH3)2)] to
calculate the charge.Firstly I use the command"antechamber" to obtain the
gaussian input file(ligand.gjf),then make optimization and calculate the
single-point energy.Finally I want to use the output file(ligand_esp.log) of
calculating the single-point energy to get the ligand.prepi and
ligand.frcmod file.But I get the wrong ligand.prepi file which has no the
parameter of FE atom .Who can help me to solve this problem,I will
appreciate your kind very much.
The content of the ligand.prepi file is :
0 0 2
This is a remark line
molecule.res
MOL 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 C2 c3 M 3 2 1 1.540 111.208 180.000 -0.125101
5 H4 h1 E 4 3 2 1.093 28.320 -147.046 0.083372
6 H5 h1 E 4 3 2 1.093 131.538 -103.425 0.083372
7 H6 h1 E 4 3 2 1.092 84.482 7.295 0.083372
8 S2 ss M 4 3 2 1.831 111.732 118.207 -0.157380
9 C30 cf M 8 4 3 1.795 102.572 -33.899 0.060221
10 C31 c2 B 9 8 4 1.344 118.466 139.147 -0.259126
。。。。。。
。。。。。。
。。。。。。
。。。。。。
77 H34 hc E 76 75 70 1.093 110.776 -138.770 0.055563
78 H35 hc E 76 75 70 1.094 110.514 -19.218 0.055563
79 C38 c3 M 76 75 70 1.562 110.384 102.395 -0.068807
80 H36 hc E 79 76 75 1.092 111.987 -111.506 0.049865
81 H37 hc E 79 76 75 1.096 111.599 8.491 0.049865
82 C39 c M 79 76 75 1.604 112.479 125.042 0.537888
83 O4 o E 82 79 76 1.244 110.419 154.069 -0.482980
84 O3 o M 82 79 76 1.249 116.685 -28.454 -0.482980
85 X 1 0 1 3.470 nan -1630.319 0.000000
86 X 1 0 1 3.470 nan-93410.396 0.000000
87 X 1 0 1 3.470 nan-5352021.561 0.000000
88 X 1 0 1 3.470 nan-306648252.537 0.000000
89 X 1 0 1 3.470 nan-17569650965.154
0.000000
90 X 1 0 1 3.470 nan-1006666864993.138
0.000000
91 X 1 0 1 3.470 nan-57677763723649.234
0.000000
92 X 1 0 1 3.470 nan-3304692489489841.000
0.000000
93 X 1 0 1 3.470 nan-189344935466225440.000
0.000000
LOOP
C32 C9
C25 N5
C18 C19
C10 C11
C34 C35
IMPROPER
C31 C27 C30 S2
C30 H29 C31 H30
C26 C28 C27 C30
C27 C9 C28 N5
C32 C28 C9 H13
C29 C25 C26 C27
C26 C8 C25 N5
C25 C21 C8 H12
C20 C8 C21 N4
C19 C21 C20 C23
C22 C18 C19 C20
C24 C20 C23 S1
C23 H24 C24 H25
C19 C7 C18 N4
C18 C13 C7 H11
C12 C7 C13 N3
C14 C11 C12 C13
C15 C10 C11 C12
C16 O2 C17 O1
C11 C6 C10 N3
C10 C35 C6 H10
C34 C6 C35 N6
C33 C9 C32 N6
C36 C32 C33 C34
C37 C33 C34 C35
C38 O4 C39 O3
DONE
STOP
Juan Zeng
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Received on Sat Oct 09 2010 - 00:30:03 PDT
