In this tutorial, we will convert the .ac file into a .lib file.
To generate the .ac file, we will first use the RESP approach. Then, we will use the prepgen program from AMBER to generate the .prepi file. Additionally, we will manually prepare the main chain file, which identifies the backbone atoms of the molecule.
The main chain file should contain the following information:
- MAIN_CHAIN: Names of the backbone atoms
- HEAD_NAME: Names of the first terminal atoms
- TAIL_NAME: Name of the end terminal atom
- OMIT_NAME: Name of the atom to be removed from the final structure
- PRE_HEAD_TYPE: Atom type connecting to the first terminal atom
- POST_TAIL_TYPE: Atom type connecting to the end terminal atom
- CHARGE: Net charge of the molecule
To generate the .prepi file, use the command:
prepgen -i 14l.ac -o 14l.prep -rn 14L -m 14l_mc.dat
Next, create the .frcmod file to verify the bond parameters for the molecule using these commands:
parmchk2 -i 14l.prep -f prepi -o 14l.frcmod -a Y -p /home/cadd/amber20_src/dat/leap/parm/gaff.dat
parmchk2 -i 14l.prep -f prepi -o 14l.frcmod2
grep -v "ATTN" 14l.frcmod > 14l.frcmod1
Finally, create the .lib file using the Leap program by loading the necessary files:
source leaprc.gaff
loadAmberParams 14l.frcmod1
loadAmberParams 14l.frcmod2
loadamberprep 14l.prep
set 14L head 14L.1.C12
saveoff 14L 14L.lib
quit
Final Output: 14L.lib