Answers for "amber xleap tleap"

0

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
###############################
Posted by: Guest on August-11-2021

Browse Popular Code Answers by Language