amber xleap tleap
notice the diffrerent
saveAmberParm model prmtop inpcrd # to save prmtop inpcrd
savepdb model residue_fixed_rna.pdb # to save new pdb
example 1:
##### xleap file / to save new pdb #####################
source oldff/leaprc.rna.ff99
addAtomTypes {
{ "DH" "H" "sp3" }
{ "C1" "C" "sp2" }
{ "C2" "C" "sp2" }
{ "C3" "C" "sp2" }
{ "C4" "C" "sp2" }
{ "C5" "C" "sp2" }
{ "C6" "C" "sp2" }
{ "CI" "C" "sp3" }
{ "OZ" "O" "sp3" }
}
loadoff /home/lib/aa5.off
loadoff /home/lib/aa3.off
model = loadpdb residue_missing_rna.pdb
savepdb model residue_fixed_rna.pdb
quit
#######################
EXAMPLE 2:
####xleap file, create water pdb parameter and inpcrd ###############################
source oldff/leaprc.rna.ff99
source leaprc.water.tip3p
addAtomTypes {
{ "5A" "C" "sp3" }
{ "5G" "C" "sp3" }
{ "U3" "O" "sp3" }
{ "ua" "O" "sp3" }
{ "uc" "O" "sp3" }
{ "ug" "O" "sp3" } not all are here
{ "uu" "O" "sp3" }
{ "C1" "C" "sp2" }
{ "C2" "C" "sp2" }
{ "C3" "C" "sp2" }
{ "C4" "C" "sp2" }
}
addPdbAtomMap {
{ "H5'" "H5'1" } { "H5''" "H5'2" }
{ "OP1" "O1P" } { "OP2" "O2P" }
{ "H2'" "H2'1" } { "HO2'" "HO'2" }
{ "HO5'" "H5T" } { "HO3'" "H3T" }
}
set default pbradii mbondi2
loadoff /home/2d_dev/RNA_dimeric_residues_dev.lib
loadamberparams /home/2d_dev/frcmod_dev
model = loadpdb ./resname.new.pdb
addions model Na+ 0
solvateoct model TIP3PBOX 12.0
saveAmberParm model prmtop inpcrd
quit
###############################