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 - 10:30:03 PST
