AMBER Archive (2009)

Subject: [AMBER] suggestions pls

From: Jio M (jiomm_at_yahoo.com)
Date: Tue Aug 11 2009 - 12:44:19 CDT

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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