Hello,
If they're both the same molecule, then you only need to have one molecule
that you save to a library file, I was just giving the example of having 2.
If the bonds are missing, it looks like something went wrong with the
template creation step (i.e. prepin creation). You may want to have another
look at how this is done and perhaps consider using R.E.D.
Good luck!
Jason
On Fri, Sep 24, 2010 at 4:55 PM, Bozell, Joseph John <jbozell.utk.edu>wrote:
> Hi Jason,
>
> Let me see if understood your description correctly, as I am still ending
> up
> with a representation in leap that shows only a single molecule with atoms
> represented as diamonds and no explicit bonds
>
> 1) Load two identical molecules into leap from antechamber:
>
> loadamberprep abxylal.prepin
> saveoff Molecules.lib
> loadamberprep abxylal1.prepin
> saveoff Molecules.lib
>
> result: a library file that appears to contain all necessary info for the
> two molecules. NOTE: I used the prepin files generated from antechamber and
> did not generate mol2 files since those were what I had available.
>
> 2) use packmol to generate a combined pdb from the two pdb files that were
> also used to generate the Molecules.lib file, using the same names for the
> residues that were used in step 1.
>
> result: combined file with TER card between the two residues/molecules
>
> 3) load the library:
>
> loadoff Molecules.lib
>
> 4) define the entire array:
>
> total_mol=loadpdb abxylalpair.pdb
>
> Output from leap:
>
> Loading PDB file: ./abxylalpair.pdb
> - - residue 1: duplicate [C1] atoms (total 2)
> - - residue 1: duplicate [C10] atoms (total 2)
> - - residue 1: duplicate [C11] atoms (total 2)
>
> ...<multiple similar lines removed>
>
> Warning: Atom names in each residue should be unique. (Same-name atoms are
> handled by using the first occurrence and by ignoring the rest. Frequently
> duplicat atom names stem from alternate conformations in the PDB file.)
>
> Unknown residue: UNK number: 0 type:Terminal/last
> ..relaxing end constraints to try for a dbase match
> -no luck
> Creating new UNIT for residue: UNK sequence:1
> Created a new atom named: O1 within residue: .R<UNK 1>
> Created a new atom named: O2 within residue: .R<UNK 1>
> Created a new atom named: H2O within residue: .R<UNK 1>
>
> ...<multiple similar lines removed>
>
> Total atoms in file: 132
> The file contained 65 atoms not in residue templates
>
> 5) observe molecule
>
> edit total_mol
>
> Result: a single molecule (or two identical superimposed molecules?) with
> atoms represented by diamonds and no explicit bonds.
>
> I apparently went awry somewhere, but I am curious about placing two
> identical molecules generated from antechamber into "Molecule.lib".
> Wouldn't
> that lead to identical coordinates for the atoms?
>
> Still trying...and thanks again,
>
> Joe Bozell
> University of Tennessee
>
>
> On 9/24/10 9:13 AM, "Jason Swails" <jason.swails.gmail.com> wrote:
>
> > Hello,
>
> My suggestion is to take each separate small molecule, parameterize it
> > using
> antechamber if that works for you (maybe use R.E.D. if you need
> > more
> stringent charge derivation), then load it into leap and use the
> > "saveoff"
> procedure to save an amber library file. For example, suppose you
> > have 2
> small molecules molecule1.pdb and molecule2.pdb. Use R.E.D. or
> > antechamber
> as you will, and get the files molecule1.mol2 and molecule2.mol2
> > with
> partial charges for each atom. Then load them into leap as such:
>
> mol1 =
> > loadmol2 molecule1.mol2
> mol2 = loadmol2 molecule2.mol2
>
> saveoff mol1
> > Molecules.lib
> saveoff mol2 Molecules.lib
>
> This will create a library file
> > "Molecules.lib" that has all of the bonding
> and charge information for each of
> > your molecules. Then you can use packmol
> to create your combined PDB file,
> > which should have the molecules in
> Molecules.lib each with the same residue
> > name and atom names. Then, you can
> load this library into leap:
>
> loadoff
> > Molecules.lib
>
> total_mol = loadPDB packmol_structure.pdb
>
> And then you just
> > have to make sure that you have parameters for all of the
> atom types and
> > bonds/angles/dihedrals. You can use parmchk on each of the
> original mol2
> > files to get these.
>
> Hope this helps,
> Jason
>
> On Fri, Sep 24, 2010 at 9:02 AM,
> > Bozell, Joseph John <jbozell.utk.edu>wrote:
>
> > Thanks very much for the lead
> > on Packmol...nice little program. I generated
> > a pdb file that contained a
> > pair of the molecules I want to work with, and
> > it would be a simple matter
> > to generate a multi-molecular array, solvated
> > or
> > unsolvated, in the same
> > manner.
> >
> > However, if I can request a little more handholding, it appears
> > that I am
> > still at the same point that I was earlier. The resulting packmol
> > file (or
> > any file containing 5, 15, 100 identical molecules that might be
> > generated
> > in Packmol) is effectively a pair of ³non-standard residues², and
> > as
> > implied
> > in the manual and tutorials, needs to have the force field
> > parameters and
> > structural information that are generated in antechamber,
> > right? Yet
> > antechamber, according to the info on the mail archives, is
> > generally only
> > useful up to around 100 atoms (this pair would have 132
> > atoms), and per
> > David Case's earlier reply, only intended for operation on a
> > single
> > molecule
> > (and it works beautifully under those conditions, BTW).
> > Nonetheless, when I
> > enter either the pdb file containing the molecular pair
> > generated by
> > packmol
> > or an earlier pdb file of the pair generated in
> > Gaussian into antechamber,
> > everything runs as expected and a prepin file is
> > generated:
> >
> > antechamber i abxylalpair.pdb fi pdb o abxylalpair.prepin
> > fo prepi c
> > bcc s 2
> >
> > But when parmchk is run on the prepi file:
> >
> >
> > parmchk i abxylalpair.prepin f prepi o abxylal.frcmod
> >
> > I receive a
> > ³segmentation fault² error message immediately.
> >
> > Am I missing the point of
> > Packmol? Does the pdb file that it generates
> > allow
> > you to go directly to
> > LEaP and generate the coordinate and topology files
> > for sander? It would
> > seem not, since an attempt to enter the molecular file
> > (with a TER card
> > inserted between the two molecules/"residues") into LEaP:
> >
> > abxylal =
> > loadpdb ³abxylalpair.pdb²
> > edit abxylal
> >
> > LEaP creates all 132 atoms
> > leading to a representation with small diamonds
> > for the atoms but no bonds
> > (connectivity) between them. This isn¹t
> > surprising with two nonstandard
> > residues. It would seem that the most
> > direct
> > approach would still be to
> > generate all atomic coordinates and charges in
> > antechamber on a single
> > molecule, and then create several clones of the
> > original at different
> > coordinates in space so that it could be interpreted
> > correctly in LEaP. But
> > am I asking for a feature not available in the
> > software?
> >
> > Sorry for the
> > continuing questionsŠthe Amber family of programs runs
> > smoothly for a single
> > simple molecule, and I am trying to fill in
> > substantial gaps in my
> > understanding of program operation so that I can
> > build more complex
> > systems.
> >
> > Joe Bozell
> > University of Tennessee
> >
> > On 9/23/10 10:13 AM, "M.
> > L. Dodson" <activesitedynamics.comcast.net>
> > wrote:
> >
> > > See below.
> > > On
> > Sep 23, 2010, at 8:46 AM, Bozell, Joseph John wrote:
> > >
> > >> Thanks for the
> > initial feedback...I guess I'm still not clear on the
> > steps
> > >> necessary
> > to execute the simulation I want. By following the manual and
> > >> various
> > online tutorials, I am able to successfully carry out
> > antechamber on
> > >> a
> > **single** copy of my molecule to generate charges, and can then
> > minimize
> >
> > >> the molecule, solvate it, and generate an MD simulation and
> >
> > movie...quite
> > >> straightforward and effective.
> > >>
> > >> However, I now
> > want to generate an appropriate set of files,
> > coordinates,
> > >> charges,
> > etc. that contain 2 (or more) copies of this same molecule,
> > solvate
> > >>
> > them, and carry out an MD simulation to see how/if they interact as a
> >
> > probe
> > >> of the first steps in self assembly. Is there a simple way to take
> > the
> > >> optimized structure generated in amber for a single molecule and
> > just
> > clone
> > >> multiple copies of it for evaluation in an MD run? Xleap
> > does not appear
> > to
> > >> have a way to carry out a molecular copy step, or
> > the ability to arrange
> > an
> > >> array of molecules in various conformations.
> > Sirius 1.2 allows me to
> > import
> > >> a couple of molecules and position them
> > independently, but does not seem
> > to
> > >> be able to save the resulting
> > molecular pair as a single file of
> > coordinates
> > >> (maybe I haven't dug
> > deeply enough into its operation??). The closest
> > >> analogies I've seen
> > involve docking a substrate in an enzyme, but I have
> > >> been unable to
> > translate those methodologies to the simpler molecules
> > I'm
> > >> working
> > with.
> > >>
> > >> Again, thanks for any guidance,
> > >>
> > >> Joe Bozell
> > >>
> > University of Tennessee
> > >
> > > There are ways of getting LEaP to do what you
> > want, I believe, but the
> > packmol
> > > program
> > (http://www.ime.unicamp.br/~martinez/packmol/<http://www.ime.unicamp.br/%7Emartinez/packmol/>
> <http://www.ime.unicamp.br/%7Emar
> > tinez/packmol/>)
> > was created to do
> > > exactly what you want. Look at the
> > example of a mixed urea-water box,
> > IIRC.
> > >
> > > Of course you will need the
> > concentration you want to simulate -> the
> > number
> > > of
> > > molecules of
> > your solute in the simulation cell. Plus the number of
> > waters to
> > >
> > achieve a density of ~1.0. My experience is that simulation cells
> > created
> >
> > > with
> > > packmol drop precipitously in energy in the first few steps of
> > dynamics
> > due to
> > > reorientation of the molecules leading to a lower
> > electrostatic term, so
> > > an initial short dynamics run at 100K is a good
> > (but not strictly
> > necessary)
> > > idea. Then proceed on with the regular
> > equilibration of temperature,
> > density,
> > > etc.
> > >
> > > Since simulation
> > systems set up with packmol start out containing
> > solvent, if
> > > you need a
> > vacuum prmtop (e.g., for postprocessing analysis), you will
> > have to
> > >
> > strip the solvent, then generate the prmtop on the stripped PDB. Kind
> of> >
> > backwards to the ordinary way of doing things.
> > >
> > > Hope this helps,
> > >
> > Bud Dodson
> > >
> > >> ------ Forwarded Message
> > >> From: Joe Bozell
> > <jbozell.utk.edu>
> > >> Date: Wed, 22 Sep 2010 14:20:36 -0400
> > >> To:
> > "amber.ambermd.org" <amber.ambermd.org>
> > >> Subject: MD on an array of small
> > molecules
> > >>
> > >> I am attempting to use Amber for MD runs on a collection
> > of small
> > molecules
> > >> to observe their interaction during a self assembly
> > process. I am able
> > to
> > >> carry out MD runs on a single molecule in a water
> > shell using
> > antechamber
> > >> and subsequent steps. However, how does one
> > carry out the same process
> > on
> > >> multiple copies of a single molecule
> > within a solvent box?
> > >>
> > >> I have a pdb file for a pair of these
> > molecules, and have used
> > antechamber
> > >> to generate a prepi file. However,
> > parmchk on the resulting file gives a
> > >> "segmentation fault" message,
> > suggesting that the number of atoms may be
> > too
> > >> large.
> > >>
> > >> Is
> > there a general method for carrying out this type of experiment
> > within
> > >>
> > Amber?
> > >>
> > >> Thanks,
> > >>
> > >> Joe Bozell
> > >> University of Tennessee
> >
> > >>
> > >>
> > >> ------ End of Forwarded Message
> > >>
> > >>
> > >>
> > _______________________________________________
> > >> 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
> >
>
>
>
> --
> >
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Graduate
> > Student
> 352-392-4032
> _______________________________________________
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> > list
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>
>
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>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Fri Sep 24 2010 - 14:30:03 PDT
