AMBER Archive (2007)

Subject: Re: AMBER: antechamber

From: Francesco Pietra (chiendarret_at_yahoo.com)
Date: Tue Jul 10 2007 - 02:04:39 CDT

"if it works".This is the point: it worked for minimization, may be failure to
perform MD is just where it then failed to work, answering that it can not find
&cntrl.

As I have posted to Ross Walker & Amber, I'll try with the intact pdb, before
doing the two fragments.

Yes, at the moment I have to overcome the problem of large molecules (the one
now, 98-atoms, is the very smallest) without repeating units. I had learned
with other programs how to make such molecules into fragments in order to
provide RESP via HF-6-31G*. Cutting where chemical intuition suggests to cut.

Dealing with the biopolymer will be the second stage: my "organic" molecules
interact with receptors, and this is my final goal. A long way, I can foresee.
Perhaps one should also accept that H2O is not ubiquitous, many regulations of
cellular processes occur in lypophilic environments, even when the main of the
biopolymer is into an aqueous environment.

Thanks

francesco

--- "M. L. Dodson" <mldodson_at_houston.rr.com> wrote:

> Francesco Pietra wrote:
>
> > I have treated with Amber9/Antechamber a molecule (natural
> > product, 98 atoms) made of two residues (because I had used
> > another suite of programs to calculate RESP charges, which
> > required to make smaller residues, and pdb atom names were
> > correct).
> >
> > I expected failure of antechamber. Actually, it prepared valid
> > parameter and coordinate files, that allowed correct
> > minimizations."list" on the prepin file showed as new unit the
> > first of the two residues, in three capital letters. At all
> > stages, generation of pdb files gave the correct molecule on
> > VMD.
> >
> > Perhaps what I did is not the equivalent of what is here warned
> > about, althoug my molecule is seen as two residues on the
> > original suite where the arragement was done.
> >
> > francesco pietra
> >
>
> Hey, if it works, ... However, I think the point is that the
> tools in the AMBER suite have specific things that they do. These
> things are implicitly (actually quite explicitly) related to the
> "model" of the kinds of molecules AMBER has been most often used
> to simulate: biopolymers. That does not mean you cannot use AMBER
> to simulate other molecule types, though. In the AMBER way of
> looking at the world, molecules are small (e.g., ligands of
> binding proteins) or polymers. Polymers are composed of
> "residues" (e.g., nucleotide or amino acid residues). To compose
> the input for the simulation programs (primarily sander and
> pmemd), you use LEaP (i.e., tleap or xleap; the acronym relates
> back to three older and obsolete AMBER programs). And of course
> the residues are composed of atoms. So the hierarchy of things
> AMBER knows about are atoms, residues and polymers. Ligands and
> other small molecules can be thought of as residues that are
> closed shell in the quantum chemistry sense.
>
> So how do we get new residues? We use antechamber (or, these
> days, maybe RED II or RED III). To create a residue descriptor,
> you need the partial atomic charges which you get with a quantum
> chemistry package, GAMESS or Gaussian mostly. But you need to do
> a closed shell calculation with the QM package, so you may need to
> add "capping residues". E.g., say we had a new amino acid
> residue, XYZ. We might do a QM calculation on the closed shell
> polymeric structure, {ACE XYZ NME}. Then to calculate the partial
> charges of XYZ, we would constrain the atomic charges of ACE and
> NME to 0.0 when running resp and define "connect" atoms where
> other residues are connected to form the polymer structure.
> Antechamber automates the steps in this new residue definition
> procedure. A closed shell ligand or other small molecule is just
> a residue with no connect atoms in this way of looking at things.
>
> So the "AMBER way" to handle new molecules is to use antechamber
> (or RED) to generate residue descriptors, then use LEaP to put the
> residues together to generate the final molecules to be simulated,
> together with counterions and solvent molecules if desired.
>
> You can probably do it other ways, but this is the way I think of
> when describing the "Amber way" of doing things. All of this is
> in the documentation, but maybe not in two adjacent paragraphs.
>
> Bud Dodson
>
> >
> > --- "David A. Case" <case_at_scripps.edu> wrote:
> >
> >> On Mon, Jul 09, 2007, Marie Brut wrote:
> >>
> >>> I prepared a mol2 file containing the coordinates of a small double
> strand
> >>> of DNA. Then, I used antechamber to generate a prepin file but here is
> the
> >>> problem : until the end of the first strand, everything is normal, but
> >> after
> >>> the prepin file is like this :
> >> Antechamber is designed to work on single residues only. It won't work
> for
> >> multiple strand molecules. You will need to split the input for
> antehchamber
> >> up into pieces, then recombine them later in leap.
> >>
> >> ....dac
> >>
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> >
> >
> >
> >
> >
>
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> --
> M. L. Dodson
> Email: mldodson-at-houston-dot-rr-dot-com
> Phone: eight_three_two-five_63-386_one
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