Hi Tyler,
I'm after DMSO to start with, and some ionic liquids ([EMIM][OAc]). I'm
trying to figure out the method to generate the .mdl files, so I can easily
make any liquid, and I don't want to edit the files by hand as that is how
errors creep in.
Do you know if there are any repositories for .mdl files?
I found a perl script in the dat/rism/model/ folder of the amber install,
but I'm having trouble figuring out which files that needs as input
Regards
Ella
On Tue, Nov 17, 2015 at 8:56 PM, Tyler Luchko (Lists) <
tluchko.lists.gmail.com> wrote:
> Hi Ella,
>
> I’m afraid that the manual and $AMBERHOME/dat/rism1d/mdl are not up to
> date on this matter.
>
> What solvent molecules do you need MDL files for? There may be some that
> are already prepared that meet your needs.
>
> I’ll try and get the RISM formats online in the next day or so.
>
> Tyler
>
> > On Nov 17, 2015, at 7:22 AM, Ella Gale <ella.gale.gmail.com> wrote:
> >
> > Dear all,
> >
> > I want to run some simple 1DRISM calculations using 'rism1D'
> >
> > The manual (copied below) says that you need .mdl file, but does not give
> > any instructions on how to build them and link provided (which is
> supposed
> > to explain this) doesn't. In the $AMBERHOME/dat/rism1d/mdl is a perl
> script
> > which requires .parm7 and .rst7 files.
> >
> > My question: How do I create .mdl files for use with 1DRISM?
> >
> > Taken from the manual: 1D-RISM calculations require details of the some
> > bulk properties of the solvent, such as temperature and dielectric
> >
> > constant, and an explicit model of the molecular components. These are
> read
> > in from one or more .mdl
> >
> > files, depending on the composition of the solvent. Several .mdl files
> are
> > included in the Amber11 distribution
> >
> > and can be found in $AMBERHOME/dat/rism1d/mdl. These include many of the
> > explicit models for solvent and
> >
> > ions used with the Amber force fields. Other solvents models may be used
> by
> > creating appropriate MDL files. See
> >
> > http://ambermd.org/formats.html for format details.
> >
> >
> > Thanks in advance,
> >
> >
> > Regards
> >
> >
> > Ella
> > _______________________________________________
> > 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
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Nov 18 2015 - 05:00:03 PST
