Hi
thank you Alex, i will try this
regards
On Mon, Jun 4, 2012 at 3:30 PM, Alex Rodriguez <alexdepremia.gmail.com>wrote:
> Hi,
>
> you did not load the protein forcefield file. It misses something similar
> to
>
> "source leaprc.ff99SB"
>
> (modify it depending on the ff that you want to employ)
>
> A.
>
> On Mon, Jun 4, 2012 at 12:22 PM, Asma Abro 28-FBAS/MSBI/F09 <
> asma.msbi28.iiu.edu.pk> wrote:
>
> > Okay I followed the antechamber tutorial, here are the set of commands:
> > STE = loadmol2 ste.mol2
> > loadamberparams ste.frcmod
> >
> > saveoff STE ste.lib
> >
> > saveamberparm STE ste.prmtop ste.inpcrd
> >
> > for creating topology and coordinate files:
> >
> > source leaprc.gaff
> >
> > loadamberparams ste.frcmod
> > loadoff ste.lib
> >
> > complex = loadpdb
> > Dock_ste.pdb<
> > http://ambermd.org/tutorials/basic/tutorial4b/files/1FKO_trunc_sus.pdb>
> > saveamberparm complex Dock_ste.prmtop Dock_ste.inpcrd
> >
> > and with this last command error occurs
> >
> >
> >
> > On Mon, Jun 4, 2012 at 3:09 PM, Alex Rodriguez <alexdepremia.gmail.com
> > >wrote:
> >
> > > 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 - 04:00:03 PDT
