I need to generate force field for an organic molecule with a strained structure. The ring has C=O group attached to it with an angle 90 degree. I tried OPLS, GAFF and CGenFF , but in all the cases, the angles obtained are not correct. Can anyone suggest me some method for forcefield generation for such a system ?
When I go to work with binders, I do the following steps.
$ source /home/**USER**/amber20/amber.sh
$ antechamber -i LIG.pdb -fi pdb -o LIG.mol2 -fo mol2 -c bcc -s 2 -nc 1
$ mkdir CAPITALS
$mv ANTECHAMBER_* CAPITALS/
$mv ATOMTYPE.INF CAPITALS/
$mv sqm.* CAPITALS/
$ parmchk2 -i LIG.mol2 -f mol2 -o LIG.frcmod
$ tleap -f /home/**USER**/amber20/dat/leap/cmd/oldff/leaprc.ff99SBildn
> source leaprc.gaff
> loadamberparams /home/**USER**/**DIR**/LIG.frcmod
> BUP = loadmol2 /home/**USER**/**DIR**/LIG.mol2
> check LIG
> saveamberparm LIG lig.prmtop lig.inpcrd
> quit
$ acpype -x lig.inpcrd -p lig.prmtop -c user -o gmx
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