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
> >> >
> >>
> >>
> >>
> >> _______________________________________________
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> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >>
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> >
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>
>
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Received on Wed Nov 09 2011 - 07:00:04 PST
