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 - 04:00:02 PDT
