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/) 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
>>
>>
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Received on Fri Sep 24 2010 - 06:30:06 PDT
