Running Antechamber for a new modified Amino Acid

S-benzylated-Cysteine  parameter generation

Using Amber 12 /AmberTools13/ Gaussian-09

Take the non-std residue attached to two adjacent amino acids (AA)
and create tripeptide.pdb from the original crystal structure containing the modified AA.

Steps to follow:-

Open xleap and do the following
Note: if having problem in Menu bars in Xleap, make sure the NUM LOCK key is OFF before starting Xleap

> source leaprc.ff12SB
> AA = loadmol2 BCS_final.mol2
> edit AA to remove the ajacent AA's.
Now added hydrogen to BCS . two H-atoms gets added. one for  NH and one for CO atoms.

Saved pdb in xleap
> savepdb AA BCS_AA.pdb
> quit

Used it as input to Antechamber to generate a DAT file.

user@localuser$ antechamber -i BCS_AA.pdb -fi pdb -o  BCS_AA_char.dat -fo gcrt -gv 1 -ge BCS_AA.gesp

Run GAUSSIAN-09 on the DAT file
user@localuser$  g09 BCS_AA_char.dat > BCS_AA_char.out

Use the OUT file to generate ESP file using espgen
user@localuser$ espgen -i BCS_AA_char.out -o BCS_AA_char.esp

Use ESP file to generate PREPIN file using Antechamber
user@localuser$ antechamber -i BCS_AA_char.out -fi gout -o BCS_AA_char.prepin -fo prepi -c resp -s 2 -rn BCS -at amber -nc 0

Note: above " i used "0" for flag -nc since the AA is neutral charge.
For negative charge modified AA in the likes of GLU/ASP -nc -1; Similarly for ARG/LYS like AA use "+1"

Use parmchk to test if all the parameters we require are available.
parmchk -i BCS_AA_char.prepin -f prepi -o BCS_AA_char.frcmod

Open xleap
>Loadoff BCS_AA_char.prepin

Enter "list" to see if BCS is added
>list
Edit BCS and delete the extra H atoms added.
>edit BCS

#check for charge after deleting atoms.
>charge BCS
Since my molecules net charge should be "0"
I had to add +0.3XXX to "N" to make the net charge "0"
This is done by selecting the atoms in Xleap.-> Edit-> Selected Atoms
which displays a table. Both 1st and 2nd column can be appropriately changed to suit ur needs.


Also change N-terminal N TYPE from "NT" to "N"
Save table by  "Save and Quit
-------------------------------------------------
Check if all is well by loading the tripeptide with BCS in middle(PRO_BCS_VAL.pdb) in tleap
using the following xleap script

xleap -s -f tleap.in

---------tleap.in------------
verbosity 2
logFile logsteps.x
source /usr/soft/amber12/dat/leap/cmd/leaprc.ff12SB
loadamberparams BCS_AA_char.frcmod
loadoff BCS_AA_char.lib
res = loadpdb ../tripep.pdb
saveAmberParm res res.prmtop res.inpcrd
--------------
No error should be displayed, Ur ready now

Happy Simulation  of your protein with a non-standard residue.