Hi All
I have a question about a command "saveamberparm" in "tleap".
I have a pdb file which contains a protein, bound waters and a ligand in this order. In order to differentiate the bound waters from solvent waters, I named the bound waters as "CTW" instead of "WAT, HOH, TP3" and created a library file "CTW.lib" which contains the same information as "TP3" in "solvent.lib". In the pdb file, residue number and atom number are assigned sequentially. In "tleap", I executed the following commands
source leaprc.ff99
loadoff CTW.lib
loadamberprep ligand.prep
loadamperparams frcmod
pdb = loadpdb target.pdb
saveamberparm pdb target.top target.x
Whereas the original pdb file contains a protein, bound waters, and a ligand, its output contains the protein, the ligand, and bound waters in this order. It seems to me that "saveamberparm" command kindly sorted them even if I gave a special residue name to bound waters. I would like to keep the order of protein, bound waters and ligand. Is there anyway to avoid the sorting? Did I make any mistake?
Thank you in advance
Masaki Tomimoto
Received on Thu Aug 15 2002 - 13:25:45 PDT
