Easy automated way to fix is this remove ligand from the PDB. Save the PDB
as rec.pdb open it by MMV ( Molegro Molecular Viewer) . Save the receptor
and overwrite on rec.pdb. Use any external programme such as chimera to
remove H from the receptor and run tleap again it will work. If you prepare
your receptor using MMV or even by GLIDE it will assign proper residue
index, atom type and connection which will resulted in smooth tleap.
On Thu, Jul 3, 2014 at 11:45 AM, Vishal Nemaysh <
vishal.bioinfotech.gmail.com> wrote:
> Hi,
>
> I am a newbie to use the AMBER 12 and doing practice from the tutorial
> *SUSTIVA
> Amber module* by using following link (
> http://ambermd.org/tutorials/basic/tutorial4b/) . I have encountered the
> following error while running tleap to create the topology and coordinate
> file for Sustiva-RT complex. Kindly suggest me how to overcome this
> error.Thanks in advance
>
> FATAL: Atom .R<VAL 241>.A<C 3> does not have a type.
> FATAL: Atom .R<VAL 241>.A<O 4> does not have a type.
> FATAL: Atom .R<VAL 241>.A<CB 5> does not have a type.
> FATAL: Atom .R<VAL 241>.A<CG1 6> does not have a type.
> FATAL: Atom .R<VAL 241>.A<CG2 7> does not have a type.
> FATAL: Atom .R<GLN 242>.A<N 1> does not have a type.
> FATAL: Atom .R<GLN 242>.A<CA 2> does not have a type.
> FATAL: Atom .R<GLN 242>.A<C 3> does not have a type.
> FATAL: Atom .R<GLN 242>.A<O 4> does not have a type.
> FATAL: Atom .R<GLN 242>.A<CB 5> does not have a type.
> FATAL: Atom .R<GLN 242>.A<CG 6> does not have a type.
> FATAL: Atom .R<GLN 242>.A<CD 7> does not have a type.
> FATAL: Atom .R<GLN 242>.A<OE1 8> does not have a type.
> FATAL: Atom .R<GLN 242>.A<NE2 9> does not have a type.
> FATAL: Atom .R<PRO 243>.A<N 1> does not have a type.
> FATAL: Atom .R<PRO 243>.A<CA 2> does not have a type.
> FATAL: Atom .R<PRO 243>.A<C 3> does not have a type.
> FATAL: Atom .R<PRO 243>.A<O 4> does not have a type.
> FATAL: Atom .R<PRO 243>.A<CB 5> does not have a type.
> FATAL: Atom .R<PRO 243>.A<CG 6> does not have a type.
> FATAL: Atom .R<PRO 243>.A<CD 7> does not have a type.
> Failed to generate parameters
> Parameter file was not saved.
>
> --
> Vishal
> Research Scholar,
> Neuropharmaceutical Chemistry lab.,
> Dr. B. R. Ambedkar Center for Biomedical Research,
> University of Delhi, Delhi-110007
> Email: *vishal.bioinfotech.gmail.com <vishal.bioinfotech.gmail.com>*
> Phone: 91-11-27662778 Mobile: 91+9650736653
> _______________________________________________
> AMBER mailing list
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> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Thanks & Regards;
Soumendranath Bhakat
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Received on Thu Jul 03 2014 - 05:00:02 PDT
