Thanks, Lachelle. I had tried to run the Leap input file just to check if I
could generate the topology file for the sucrose molecule. However, tLeap
could not find many of the files it was trying to load. As you say, some may
not be required, so I'll remove these and see what happens, (not today
though, it's late :D )
- Jose
On Tue, Nov 23, 2010 at 8:48 PM, Lachele Foley (Lists) <lf.list.gmail.com>wrote:
> If you download the "leap input file" you will see the instructions
> the builder used to build the sucrose. Then, you can just add those
> into a larger build. For example, in the one I just built (sucrose
> can be built two ways), the file says:
>
> amber_seq = sequence { 1GA 0CU }
>
> The leap input file also loads a lot of other stuff, some of it not
> relevant to sucrose, some of it required. Check out the message at
> the link below for an example of how to generate a topology file
> containing more than one molecule.
>
> http://archive.ambermd.org/201009/0037.html
>
> You should only need the first two steps unless you need to specify
> the number of water molecules. You will need to add a "saveamberparm"
> command to the first step.
>
> If this is Amber 11, you must use sleap to generate your input files
> and use the "set default write14scale on" directive in the input file.
> If it is an earlier version of Amber, you should set scee and scnb
> to 1.0 in your simulation control input files.
>
> :-) Lachele
>
> On Tue, Nov 23, 2010 at 8:27 PM, Jose Borreguero <borreguero.gmail.com>
> wrote:
> > I used the Amber/Glycam input configurator
> > tool<http://glycam.ccrc.uga.edu/AMBER>(
> > http://glycam.ccrc.uga.edu/AMBER/) and obtained a topology file for the
> > sucrose molecule. However, I have to simulate the sucrose in the presence
> of
> > another molecule, so the topology file of the sucrose by itself will not
> do.
> > Maybe there is a way of using the topology file in order to obtain the
> lib
> > and frcmod files for the sucrose "residue", but I ignore it.
> >
> > - Jose
> >
> > On Tue, Nov 23, 2010 at 8:07 PM, Lachele Foley (Lists) <
> lf.list.gmail.com>wrote:
> >
> >> If you plan to use GLYCAM (and you probably should), there isn't a
> >> specific frcmod or lib.
> >>
> >> See the section in the AmberTools manual on building oligosaccharides.
> >> Is this Amber 11 or a previous version?
> >>
> >>
> >> On Tue, Nov 23, 2010 at 5:56 PM, Jose Borreguero <borreguero.gmail.com>
> >> wrote:
> >> > Dear Amber users,
> >> >
> >> > Has anybody used the lib and frcmod files for sucrose ? I can't find
> them
> >> > anywhere.
> >> >
> >> > Best regards
> >> > Jose M. Borreguero
> >> > _______________________________________________
> >> > AMBER mailing list
> >> > AMBER.ambermd.org
> >> > http://lists.ambermd.org/mailman/listinfo/amber
> >> >
> >>
> >>
> >>
> >> --
> >> :-) Lachele
> >> Lachele Foley
> >> CCRC/UGA
> >> Athens, GA USA
> >>
> >> _______________________________________________
> >> 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
> >
>
>
>
> --
> :-) Lachele
> Lachele Foley
> CCRC/UGA
> Athens, GA USA
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Tue Nov 23 2010 - 18:30:03 PST
