ok- but addles won't help with this. you'll need to find a way or write a
script to fix the input pdb file. how you do that depends on where the pdb
file came from- I suspect it doesn't relate to Amber.
On Wed, Nov 9, 2011 at 9:50 AM, Jennifer Brookes <j.brookes.ucl.ac.uk>wrote:
> Thanks again, the problem is when I try this (using leap for the whole pdb)
> I get issues reading in the pdb (the error reads that there are duplicate
> atoms) when I use:
>
> LIG = loadpdb 60mer.pdb
>
> At the moment in my .pdb I have the atom numbers 1- 13440 (60x224), though
> each dimer of 224 atoms is separated by TER, resname LIG (for all dimers)
> and residue number 1 (again for all dimers). So for the combination of
> these
> three fields there should be no duplicates. I have tried renumbering and
> formatting but don't seem able to modify the .pdb so that it is read
> correctly.
>
> With thanks,
> Jenny
>
>
>
> -----Original Message-----
> From: Carlos Simmerling [mailto:carlos.simmerling.gmail.com]
> Sent: Wednesday, November 09, 2011 9:36 AM
> To: AMBER Mailing List
> Subject: Re: [AMBER] addles "old coordinate file not specified"
>
> the issue is still that you are not giving addles any information about the
> arrangement of the 60mer.
>
> unless I misunderstand, you should use the frcmod file that worked properly
> for the dimer, and just repeat the same procedure with leap except load in
> the pdb of the 60mer. what happens when you do this? addles and neb are not
> related to what you want to do (as far as I can tell).
>
>
> On Tue, Nov 8, 2011 at 1:16 PM, Jenny C Brookes <j.brookes.ucl.ac.uk>
> wrote:
>
> > Thank you for the email.
> >
> > > when you say "parameterizing the dimer" do you mean developing force
> > field
> > > parameters, or making a prmtop?
> >
> > I mean both. I make an frcmod file that is particular to the dimer and
> > make a dimer.prmtop and inpcrd from that using leap, all successfully.
> >
> >
> > > 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.
> >
> > That is why I was using pack=2 in the addles.in file and concatenating
> > the input coordinate files (similar to the neb tutorial), but having
> > no success printing the end .inpcrd file.
> >
> >
> > > 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.
> >
> > Except the entire system is just 60X repeated dimer units with the
> > same parameters.
> >
> > With thanks,
> > Jenny
> >
> >
> > > 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
> > >> >> > >
> > >> >> > >
> > >> >> > >
> > >> >> > >
> > >> >> > >
> > >> >> > >
> > >> >> > >
> > >> >> > > _______________________________________________
> > >> >> > > AMBER mailing list
> > >> >> > > AMBER.ambermd.org
> > >> >> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >> >> > >
> > >> >> > _______________________________________________
> > >> >> > AMBER mailing list
> > >> >> > AMBER.ambermd.org
> > >> >> > http://lists.ambermd.org/mailman/listinfo/amber
> > >> >> >
> > >> >> >
> > >> >> > _______________________________________________
> > >> >> > AMBER mailing list
> > >> >> > AMBER.ambermd.org
> > >> >> > http://lists.ambermd.org/mailman/listinfo/amber
> > >> >> >
> > >> >> _______________________________________________
> > >> >> AMBER mailing list
> > >> >> AMBER.ambermd.org
> > >> >> http://lists.ambermd.org/mailman/listinfo/amber
> > >> >>
> > >> >>
> > >> >> _______________________________________________
> > >> >> AMBER mailing list
> > >> >> AMBER.ambermd.org
> > >> >> http://lists.ambermd.org/mailman/listinfo/amber
> > >> >>
> > >> > _______________________________________________
> > >> > AMBER mailing list
> > >> > AMBER.ambermd.org
> > >> > http://lists.ambermd.org/mailman/listinfo/amber
> > >> >
> > >>
> > >>
> > >>
> > >> _______________________________________________
> > >> AMBER mailing list
> > >> AMBER.ambermd.org
> > >> http://lists.ambermd.org/mailman/listinfo/amber
> > >>
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> >
> >
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
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Received on Wed Nov 09 2011 - 07:00:05 PST
