OK so it seems that the only way to do this is to tediously write out larger and larger prmtop files, just repeating the force field data, to produce the input.
Steve
Dr S Bailey
Department of Physics
Lancaster University UK
Email: s.bailey.lancaster.ac.uk
Tel: +441524592844
-----Original Message-----
From: cieplak.cgl.ucsf.edu [mailto:cieplak.cgl.ucsf.edu]
Sent: 12 June 2013 16:33
To: AMBER Mailing List
Subject: Re: [AMBER] prmtop
There is nothing about solvateDontClip command in LeaP documentation.
Piotr
> 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 - 09:00:03 PDT
