when you say "parameterizing the dimer" do you mean developing force field
parameters, or making a prmtop?
in any case, you should still almost certainly use the 60-mer (or whatever)
using leap, not addles. if you don't give amber the pdb file with all 60
units it will have no idea where to place them in space.
and no, you can't use just the dimer prmtop to simulate everything. the
prmtop has much more information than just atom info- it tells Amber how
many atoms, how many residues and so on. these must correspond to the
entire system. you should try to use the same Leap procedure that you used
for the dimer, but instead give it the 60-mer pdb file and all of the other
information about force field, if any.
On Tue, Nov 8, 2011 at 11:10 AM, Jenny C Brookes <j.brookes.ucl.ac.uk>wrote:
>
>
> > no addles won't work, since it replicates the atoms in the same
> positions.
>
> I thought that would work: as long as I just do one copy (with no images
> on top of the same coordinates) for each dimer position as a trick to make
> one large inpcrd file (in the test run I was going for 2 parts but the
> idea ultimately is to go for 60) and one large prmtop file.
>
> > I'm not sure why you aren't loading the original coordinates into Leap-
> > the
> > geometry is getting lost when you only load the dimer. Maybe you can keep
> > trying to tell us what information you have and what you want to do- why
> > split into 60 mol2 files?
>
> I have one large .pdb file with 60 x dimer units. The dimers are a
> repeated unit that form 2 concentric rings. 30 in each ring. Each dimer is
> 224 atoms. I first ran a simulation parameterizing the dimer only and now
> I would like to simulate the 2 concentric rings.
>
> Since the dimer is the repeating unit then I only really need one .prmtop
> file to describe all the interactions but I need all the 60 X .inpcrd's so
> I can describe the particular geometry. I am running namd for the MD
> simulation and there does not appear to be a way to use the same prmtop
> file for several coordinates (?). So I am trying to make one large prmtop
> file and one large inpcrd file and I thought addles might be a way.
>
> I have tried using tleap to solve this problem:
>
> So I create a .lib file for the dimer:
>
> tleap -f leaprc.ff99SB
>
> source leaprc.gaff
>
> LIG=loadmol2 dimer.mol2
>
> check LIG
>
> loadamberparams dimer.frcmod (as parameterized from previous simulation)
>
> saveoff LIG dimer.lib
>
> saveamberparm LIG dimer.prmtop dimer.inpcrd
>
>
> Then to parameterize for all 60 dimers:
>
> tleap -f leap.ff99SB
>
> source leaprc.gaff
>
> loadamberparams dimer.frcmod
>
> loadoff dimer.lib
>
> ring=loadpdb ring.pdb
>
> saveamberparm ring ring.prmtop ring.inpcrd
>
> quit
>
>
> Although the .pdb file is never read correctly in the loadpdb step and the
> parameter files are never created. I have checked the .pdb is in AMBER
> compatable notation and each dimer (LIG)is separated by TER, but then
> there appears to be trouble with duplicate atom names. So I became stuck
> at this point also.
>
> Sorry If I haven't explained the problem too clearly. Any more guidance is
> much appreciated.
>
> Best wishes,
> Jenny
>
>
>
>
>
>
> >
> >
> >
> > On Mon, Nov 7, 2011 at 3:13 PM, Jennifer Brookes
> > <j.brookes.ucl.ac.uk>wrote:
> >
> >> 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
> >> > >
> >> > >
> >> > >
> >> > >
> >> > >
> >> > >
> >> > >
> >> > > _______________________________________________
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> >> > >
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Received on Tue Nov 08 2011 - 09:30:05 PST
