Dear all,
I want to study the behavior of protein And DNA in ionic liquid. I have followed this steps to make .prmtop (topology) and .inpcrd.
> /home/saikat/AMBER/amber14/bin/xleap -s -f /home/saikat/AMBER/amber14/dat/leap/cmd/leaprc.ff14SB
> source leaprc.gaff
> loadamberparams ionicliq.frcmod
> loadamberprep ionicliq.prepc
> m=loadpdb protein.pdb
or in case DNA(both pdb is made by packmol)
>m=loadpdb DNA.pdb
> set m box {60.0 60.0 60.0}
> saveamberparm m protein.prmtop protein.inpcrd (in case of protein )
> saveamberparm m DNA.prmtop DNA.inpcrd (in case of DNA)
Now my question is If I use source leaprc.gaff command for DNA and protein is it load gaff forcefield or ff14SB force field??
I want to take ff14SB force field for DNA and Protein ,AND gaff force field for ionic liquid.please suggest me my steps are correct or not . Please help me out.
Thanks and regards,
Saikat
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Aug 01 2017 - 04:00:02 PDT
