Dear amber users,
Is it ok with the following script for tleap to use the parameter files
developed by Santa Lucia Group with FF99CHI force field developed by
Yildirim et al. ?
Please suggest.
Script is as follows:
source $AMBERHOME/dat/leap/cmd/oldff/leaprc.rna.ff99
addAtomTypes {
{ "C1" "C" "sp2" }
{ "C2" "C" "sp2" }
{ "C3" "C" "sp2" }
{ "C4" "C" "sp2" }
{ "C7" "C" "sp2" }
{ "C8" "C" "sp2" }
}
loadamberparams frcmod.parmCHI
loadoff all_RNA_YST
loadamberprep 2SU.prepin
loadamberparams 2SU.frcmod
verbosity 2
S=s2u.pdb
addions S Na+ 0
solvateOct S TIP3PBOX 9.0
set default PdbWriteCharges on
check S
saveamberparm S s2u.prmtop s2u.inpcrd
logfile leap.log
savepdb S s2u_new.pdb
QUIT
Thanks
---------------------------------------------------------------------
Indrajit Deb
Kolkata, India.
Mob: +919239202278
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Received on Fri Dec 14 2012 - 00:00:02 PST
