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/%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
>
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> 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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Received on Fri Sep 24 2010 - 14:00:06 PDT
