I'm not sure if I'm understanding your question correctly but if you
already have coordinates of your molecules you can create files using
antechamber that list all of the modifications needed for the force field.
To do this I use
antechamber -i ethylene_glycol.mol2 -fi mol2 -o ethylene_glycol.prepi -fo
prepi -s 2
parmchk -i ethylene_glycol.mol2 -f mol2 -a Y -o ethylene_glycol.frcmod
which will give you frcmod and prepi files that can be loaded into leap to
give parameters for your molecules. If you just need a box filled with
your molecule you can do it in leap, this is an example that I have used
tleap -f leaprc.ff99SB
source leaprc.gaff
loadamberparams ethylene_glycol.frcmod
loadamberprep ethylene_glycol.prepi
ETG=loadpdb ETG.pdb
set ETG restype solvent
a = loadpdb ETG.pdb
solvatebox a ETG 20
savepdb a ETG_box.pdb
saveamberparm a ETG_box.prmtop ETG_box.inpcrd
There is a tutorial in amber for using antechamber if it helps:
http://ambermd.org/tutorials/basic/tutorial4b/
Hope this helps,
Sarah
On Wed, Jun 12, 2013 at 11:49 AM, Bailey, Steven
<s.bailey.lancaster.ac.uk>wrote:
> 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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> >
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> >
>
>
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Received on Wed Jun 12 2013 - 09:30:03 PDT
