Yes, that is what I would like. I have a specific geometry for the 60dimers
that I can split into 60 dimer .mol2 files and I was then hoping I could use
addles to stitch back together one .prmtop and one .inpcrd. The dimers have
long range order like a crystal lattice. If addles is not suitable and if
anyone knows of an alternative, that would be much appreciated.
With thanks,
Jenny
-----Original Message-----
From: Carlos Simmerling [mailto:carlos.simmerling.gmail.com]
Sent: Monday, November 07, 2011 1:38 PM
To: AMBER Mailing List
Subject: Re: [AMBER] addles "old coordinate file not specified"
I don't think addles will do this. It sounds like you want a tool that can
build higher-order structures, but it still isn't clear if you are looking
for a specific geometry for the 60 molecules, such as a crystal lattice.
On Mon, Nov 7, 2011 at 1:01 PM, Jennifer Brookes <j.brookes.ucl.ac.uk>wrote:
> I am using pack 2 as I have 2 coordinates in dimer.inpcrd (to create
> inpcrd for the 2 dimers) and I would like in principle to be able to
> use this tool for 60 coordinates. I don't actually want to use neb I
> was just following and modifying the instructions from the tutorial as
> a way to create .prmtop and .incrd files for many molecules with the
> same .prmtop specification (as in my first email). So I do not want
> many images of the dimer for a conformation search I just want to copy
> one so all have different coordinates. There is probably a better way, but
I do not know what it is.
>
> To run addles I have been using amber10.
>
> With thanks,
> Jenny
>
> -----Original Message-----
> From: Carlos Simmerling [mailto:carlos.simmerling.gmail.com]
> Sent: Monday, November 07, 2011 12:29 PM
> To: AMBER Mailing List
> Subject: Re: [AMBER] addles "old coordinate file not specified"
>
> not sure if this is the issue, but could it be the "pack 2" part?
> it's hard to help without knowing why you want to use addles. are you
> planning NEB? if yes, which Amber version? for Amebr 11 NEB does not
> use LES any more.
>
>
>
> On Mon, Nov 7, 2011 at 12:25 PM, Jennifer Brookes
> <j.brookes.ucl.ac.uk>wrote:
>
> > Dear Amber users,
> >
> >
> >
> > I have .prmtop and .inpcrd files for a dimer unit which is one
> > lattice unit that makes up an ordered assembly. I would like to make
> > input files for the whole assembly (x60 of the dimer unit). So I
> > have one prmtop file that describes all interactions (dimer.prmtop)
> > and several coordinate files. To do this, just to test the
> > principle, I have first tried using addles to generate the input
> > files for a pair of dimer units. So I try a script
> > addles.in:
> >
> >
> >
> > file rprm name=(dimer.prmtop) read
> >
> > file ucrcd name=(dimer.inpcrd) pack 2 read
> >
> > file wprm name (neb.prmtop) wovr
> >
> > file uwcrd name(neb.inpcrd) wovr
> >
> > action
> >
> > omas
> >
> > space numc=2 #prt 1 224 done
> >
> > *EOD
> >
> >
> >
> >
> >
> > addles < addles.in > addles.out
> >
> >
> >
> > But the inpcrd file is not read or re-written and I get the
> > following error in addles.out:
> >
> > 'Warning-old coordinate file not specified'
> >
> > 'New Coordinate file will not be created'
> >
> >
> >
> > The .prmtop file is written but not the .inpcrd file. If I create
> > the neb.inpcrd by hand and view neb.prmtop and neb.inpcrd in VMD the
> > atom assignments are all wrong for the 2 dimer units.
> >
> >
> >
> > If I follow the instructions in the 'nudged elastic band' tutorial:
> >
> >
> >
> > http://ambermd.org/tutorials/advanced/tutorial5_amber9/section3.htm
> >
> >
> >
> > I also get similar issues (the .prmtop file is generated ok, but not
> > the .inpcrd). Please does anybody see what the problem may be?
> >
> >
> >
> > With thanks,
> >
> > Jenny
> >
> >
> >
> >
> >
> >
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
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Received on Mon Nov 07 2011 - 12:30:04 PST
