I use this command to convert NITRIC OXIDE containing pdb file to mol2
antechamber -fi pdb -fo mol2 -i NIT.pdb -o NIT.mol2 -pf y
after that this file generated .<TRIPOS>MOLECULE
NIT
2 1 1 0 0
SMALL
No Charge or Current Charge
.<TRIPOS>ATOM
1 N01 4.0110 18.9270 70.5450 N01 188 NIT
0.000000
2 O02 4.4660 17.7900 70.4550 O02 188 NIT
0.000000
.<TRIPOS>BOND
1 1 2 2
.<TRIPOS>SUBSTRUCTURE
1 NIT 1 TEMP 0 **** **** 0 ROOT
I use this command to convert NITRIC OXIDE containing pdb file to mol2
antechamber -fi pdb -fo mol2 -i NIT.pdb -o NIT.mol2 -pf y
after that this file generated
then i use below command to generate the Frcmod file
parmchk -i NIT.mol2
<
http://ambermd.org/tutorials/advanced/tutorial20/files/mcpbpy_heme/1PE.mol2>
-o NIT.frcmod
<
http://ambermd.org/tutorials/advanced/tutorial20/files/mcpbpy_heme/1PE.frcmod>
-f mol2
remark goes here
MASS
N01 0.000 0.000 ATTN, need revision
O02 0.000 0.000 ATTN, need revision
BOND
N01-O02 0.00 0.000 ATTN, need revision
ANGLE
DIHE
IMPROPER
NONBON
N01 0.0000 0.0000 ATTN, need revision
O02 0.0000 0.0000 ATTN, need revision
thanks
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Received on Tue Jul 04 2017 - 21:00:03 PDT
