Hi Steve,
Amber can do this. In leap you will need to specify two "molecules" that represent the same compound, and then use the command solvateDontClip. The leap input file will look something like:
MOL = loadmol2 molecule.mol2
mol = sequence {MOL}
solv = sequence {MOL}
solvateDontClip mol solv 19.0
You can adjust the value of 19.0 until you get ~100 molecules into your box. This works well with smaller molecules (i.e. a solvent size), but for something larger (e.g. a shortened polymer chain) it becomes more problematic.
Cheers,
Karl
----- Original Message -----
From: "Steven Bailey" <s.bailey.lancaster.ac.uk>
To: amber.ambermd.org
Sent: Wednesday, June 12, 2013 3:42:46 PM
Subject: [AMBER] prmtop
Amber mailing
I am new to Amber but am a user of DLPOLY. In DLPOLY once I have created a force field for a single molecule I can then repeat that molecule as many times as I want by simply telling DLPOLY to read the force field parameters repeatedly (of course this has to agree with the coordinate file input).
How do I do this in Amber i.e. I have the mol2 file from Antechamber for 1 molecule and I then prepare a prmtop file. Is there a counter in this file to tell Amber to read it 100 times?. I have a separate routine to write out the required inpcrd.
Steve
Dr S Bailey
Department of Physics
Lancaster University UK
Email: s.bailey.lancaster.ac.uk
Tel: +441524592844
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Received on Wed Jun 12 2013 - 07:30:03 PDT
