Is still missing the leap input file, i.e. the set of instructions that you
employ in leap
A.
On Mon, Jun 4, 2012 at 12:02 PM, Asma Abro 28-FBAS/MSBI/F09 <
asma.msbi28.iiu.edu.pk> wrote:
> Thank you Alex,
>
> I am sending the three input files.
>
> P.S.: The ste.lib file is given here with simple .txt format as .lib file
> fails to send.
>
> Regards
>
> On Mon, Jun 4, 2012 at 2:54 PM, Alex Rodriguez <alexdepremia.gmail.com
> >wrote:
>
> > Hi,
> > could you send the leap input file?
> >
> > With the information in the e-mail I could tell you that may be you are
> not
> > loading the protein force field parameters/topologies, but I would need
> the
> > full leap input/output to confirm it.
> >
> > Regards
> >
> > Alex.
> >
> > On Mon, Jun 4, 2012 at 11:47 AM, Asma Abro 28-FBAS/MSBI/F09 <
> > asma.msbi28.iiu.edu.pk> wrote:
> >
> > > Hi all,
> > >
> > > I am working on the simulation of ligand-protein docked complex. After
> > > successful creation of ligand library, now I am trying to load the
> > complex
> > > with the command
> > >
> > > complex = loadpdb
> > > Dock_ste.pdb<
> > > http://ambermd.org/tutorials/basic/tutorial4b/files/1FKO_trunc_sus.pdb
> >
> > >
> > > It looks like its working fine but when I write the command
> > >
> > > saveamberparm complex Dock_ste.prmtop Dock_ste.inpcrd
> > >
> > > It gives the error:
> > >
> > > FATAL: Atom .R<PRO 227>.A<HD2 3> does not have a type.
> > > .
> > > .
> > > .
> > > .
> > > .
> > > FATAL: Atom .R<STE 289>.A<6HC4 129> does not have a type.
> > > Failed to generate parameters
> > > Parameter file was not saved.
> > >
> > > Can someone please help how to remove this error? i have checked
> archives
> > > too for the rectification of this error but my problem persists anyhow
> :(
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Received on Mon Jun 04 2012 - 03:30:03 PDT
