Hi Sidney,
Paramfit is new in AmberTools12, so you will need to install that in order
to generate bonded parameters.
Robin Betz
On Tue, Apr 17, 2012 at 12:38 AM, Sidney Elmer <paulymer.gmail.com> wrote:
> Hi,
>
> I'm wondering if there is a program in AmberTools 1.5 that is equivalent to
> paramfit? Or is it necessary to install AmberTools12 in order to
> parameterize bonding interactions? Thanks for the help.
>
> Sid
>
> On Mon, Apr 16, 2012 at 11:00 PM, Robin Betz <rbetz.ucsd.edu> wrote:
>
> > Hi Francesco,
> >
> > That helps much. I am only interested in paramfit, so that the second
> > > option is what I want. However, is it any configuration to parallelize
> > > paramfit on more that two processors?
> >
> >
> > OpenMP will automatically set the number of threads equal to the number
> of
> > processors- the output I listed just said 2 as an example. If you wish to
> > manually set the number of threads, export OMP_NUM_THREADS=*n* where n is
> > the integer number of threads to use.
> >
> > More importantly, is it any hope to adjust vdw params for atoms that
> > > are not comprised in antechamber? I mean that I plan to choose by
> > > intuition such params and hope that paramfit will correct them
> > > appropriately.
> >
> >
> > Paramfit only fits bonded forces, and does not change any nonbonded
> > parameters (vdw, hbonds, etc). I'm not too familiar with how to calculate
> > nonbonded parameters, but there seem to be a couple previous threads that
> > can help:
> > http://ambermd.org/Questions/vdw.html
> > http://archive.ambermd.org/200504/0376.html
> > http://archive.ambermd.org/201107/0357.html
> >
> > Hope this helps,
> >
> > Robin Betz
> >
> >
> > On Mon, Apr 16, 2012 at 10:28 PM, Francesco Pietra <
> chiendarret.gmail.com
> > >wrote:
> >
> > > Hi Robin:
> > > That helps much. I am only interested in paramfit, so that the second
> > > option is what I want. However, is it any configuration to parallelize
> > > paramfit on more that two processors?
> > >
> > > More importantly, is it any hope to adjust vdw params for atoms that
> > > are not comprised in antechamber? I mean that I plan to choose by
> > > intuition such params and hope that paramfit will correct them
> > > appropriately.
> > >
> > > thanks
> > >
> > > (rbetz.ucsd is not recognized by my provider)
> > >
> > > francesco pietra
> > >
> > > On Tue, Apr 17, 2012 at 12:13 AM, Robin Betz <rbetz.ucsd.edu> wrote:
> > > > Hi Francesco,
> > > >
> > > > You need to re-run the configure script in $AMBERHOME with the
> -openmp
> > > > option:
> > > > $AMBERHOME/configure -openmp gnu (or intel if you are using those
> > > > compilers).
> > > >
> > > > To only recompile paramfit with the openmp, go to
> > > > $AMBERHOME/AmberTools/src/paramfit
> > > > and run make install
> > > > Paramfit's header message will have a line saying something like:
> > > >
> > > >
> > >
> >
> *************************************************************************************
> > > > Execution started at:
> > > > | Mon Apr 16 15:11:56 2012
> > > > |
> > > > | Running OpenMP version of code using 2 processors
> > > >
> > > > if it has been compiled correctly with OpenMP support.
> > > >
> > > > Hope this helps,
> > > >
> > > > Robin Betz
> > > >
> > > >
> > > >
> > > >
> > > >
> > > > On Mon, Apr 16, 2012 at 12:47 AM, Francesco Pietra <
> > > chiendarret.gmail.com>wrote:
> > > >
> > > >> Hello:
> > > >> I have installed without errors (after commenting out line 450 of
> > > >> "configure2" as Prof Case suggested)
> > > >> serial-ambertools12/serial-amber10 in Debian amd64 in a game machine
> > > >> with six CPU's and two GTX-580 cards. I would be much interested in
> > > >> having "paramfit" parallelized. I have an installation of OpenMPI.
> > > >>
> > > >> It is not clear to me when and where "Enable this by adding the
> > > >> -openmp option to configure and rebuilding paramfit" should be done. I
> > > >> can imagine on this particular code within ambertools12,nonetheless
> a
> > > >> bit of guideline would be helpful.
> > > >>
> > > >> Thanks
> > > >>
> > > >> francesco pietra
> > > >>
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Received on Tue Apr 17 2012 - 11:30:02 PDT
