Dear AMBER users,
pls anybody give suggestions
1) I want to give environment of a {molecule + water} as a solvent to
some solute (like we normally solvate with water only). can I do like
this:
if my solute variable is "solt" and variable for solvent molecule is "solv" and both saved in abc.lib
source leaprc.gaff (also loading the frcmod files of solv and solt)
loadoff abc.lib
solvateoct solt solv 8.0 {this adds solv residues to solt }
loadoff solvents.lib
solvateoct solt TIP3PBOX 8.0
edit solt {this shows water and solv environment around solt}
firstly is this a correct method to follow, if yes then does it guarantees that TIP3P water is uniformily ditributed ?
2) {related to previous mail query} can we attach a ligand (which has H
donor and acceptor) to other molecule (also having H donor and
acceptor) in amber itself, but both are saved in different mol2 files
thanks
Jiomm
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Received on Wed Aug 19 2009 - 21:27:08 PDT
