It looks like you haven't sourced any leaprc file. Pick the force field you
want to use (i.e. ff99SB) and source that leaprc:
source leaprc.ff99SB
when you are running leap.
On Wed, Feb 2, 2011 at 2:44 PM, vani panguluri <vanipanguluri.gmail.com>wrote:
> Hi Perker,
>
> I had that .frcmod files if you need i will send that file to you...
>
> I can't understand clearly about what i need to edit in the file...
>
> also did you gave ambertools atom types
> explicitly ?--- i am unable to understand this???
>
>
>
> Regards ,
> Vani
>
>
> On Wed, Feb 2, 2011 at 1:38 PM, peker milas <pekermilas.gmail.com> wrote:
>
> > Hi Vani,
> >
> > Do you have an .frcmod file ? also did you gave ambertools atom types
> > explicitly ? I mean after you load the molecule you need to edit atom
> > types and charges etc...
> >
> > regards
> > peker
> >
> > On Wed, Feb 2, 2011 at 2:33 PM, vani panguluri <vanipanguluri.gmail.com>
> > wrote:
> > > Hello ,
> > >
> > > I am getting this error can anyone suggest me a solution.
> > >
> > > FATAL: Atom .R<ARG 2509>.A<HH22 24> does not have a type.
> > > FATAL: Atom .R<CYS 2510>.A<N 1> does not have a type.
> > > FATAL: Atom .R<CYS 2510>.A<CA 2> does not have a type.
> > > FATAL: Atom .R<CYS 2510>.A<C 3> does not have a type.
> > > FATAL: Atom .R<CYS 2510>.A<O 4> does not have a type.
> > > FATAL: Atom .R<CYS 2510>.A<CB 5> does not have a type.
> > > FATAL: Atom .R<CYS 2510>.A<SG 6> does not have a type.
> > > FATAL: Atom .R<CYS 2510>.A<H 7> does not have a type.
> > > FATAL: Atom .R<CYS 2510>.A<HA 8> does not have a type.
> > > FATAL: Atom .R<CYS 2510>.A<HB2 9> does not have a type.
> > > FATAL: Atom .R<CYS 2510>.A<HB3 10> does not have a type.
> > > FATAL: Atom .R<CYS 2510>.A<HG 11> does not have a type.
> > > FATAL: Atom .R<SER 2511>.A<N 1> does not have a type.
> > > FATAL: Atom .R<SER 2511>.A<CA 2> does not have a type.
> > > FATAL: Atom .R<SER 2511>.A<C 3> does not have a type.
> > > FATAL: Atom .R<SER 2511>.A<O 4> does not have a type.
> > > FATAL: Atom .R<SER 2511>.A<CB 5> does not have a type.
> > > FATAL: Atom .R<SER 2511>.A<OG 6> does not have a type.
> > > FATAL: Atom .R<SER 2511>.A<H 7> does not have a type.
> > > FATAL: Atom .R<SER 2511>.A<HA 8> does not have a type.
> > > FATAL: Atom .R<SER 2511>.A<HB2 9> does not have a type.
> > > FATAL: Atom .R<SER 2511>.A<HB3 10> does not have a type.
> > > FATAL: Atom .R<SER 2511>.A<HG 11> does not have a type.
> > > FATAL: Atom .R<GLU 2512>.A<N 1> does not have a type.
> > > FATAL: Atom .R<GLU 2512>.A<CA 2> does not have a type.
> > > FATAL: Atom .R<GLU 2512>.A<C 3> does not have a type.
> > > FATAL: Atom .R<GLU 2512>.A<O 4> does not have a type.
> > > FATAL: Atom .R<GLU 2512>.A<CB 5> does not have a type.
> > > FATAL: Atom .R<GLU 2512>.A<CG 6> does not have a type.
> > > FATAL: Atom .R<GLU 2512>.A<CD 7> does not have a type.
> > > FATAL: Atom .R<GLU 2512>.A<OE1 8> does not have a type.
> > > FATAL: Atom .R<GLU 2512>.A<OE2 9> does not have a type.
> > > FATAL: Atom .R<GLU 2512>.A<H 10> does not have a type.
> > > FATAL: Atom .R<GLU 2512>.A<HA 11> does not have a type.
> > > FATAL: Atom .R<GLU 2512>.A<HB2 12> does not have a type.
> > > FATAL: Atom .R<GLU 2512>.A<HB3 13> does not have a type.
> > > FATAL: Atom .R<GLU 2512>.A<HG2 14> does not have a type.
> > > FATAL: Atom .R<GLU 2512>.A<HG3 15> does not have a type.
> > > FATAL: Atom .R<SER 2513>.A<N 1> does not have a type.
> > > FATAL: Atom .R<SER 2513>.A<CA 2> does not have a type.
> > > FATAL: Atom .R<SER 2513>.A<C 3> does not have a type.
> > > FATAL: Atom .R<SER 2513>.A<O 4> does not have a type.
> > > FATAL: Atom .R<SER 2513>.A<CB 5> does not have a type.
> > > FATAL: Atom .R<SER 2513>.A<OG 6> does not have a type.
> > > FATAL: Atom .R<SER 2513>.A<H 7> does not have a type.
> > > FATAL: Atom .R<SER 2513>.A<HA 8> does not have a type.
> > > FATAL: Atom .R<SER 2513>.A<HB2 9> does not have a type.
> > > FATAL: Atom .R<SER 2513>.A<HB3 10> does not have a type.
> > > FATAL: Atom .R<SER 2513>.A<HG 11> does not have a type.
> > > FATAL: Atom .R<THR 2514>.A<N 1> does not have a type.
> > > FATAL: Atom .R<THR 2514>.A<CA 2> does not have a type.
> > > FATAL: Atom .R<THR 2514>.A<C 3> does not have a type.
> > > FATAL: Atom .R<THR 2514>.A<O 4> does not have a type.
> > > FATAL: Atom .R<THR 2514>.A<CB 5> does not have a type.
> > > FATAL: Atom .R<THR 2514>.A<OG1 6> does not have a type.
> > > FATAL: Atom .R<THR 2514>.A<CG2 7> does not have a type.
> > > FATAL: Atom .R<THR 2514>.A<H 8> does not have a type.
> > > FATAL: Atom .R<THR 2514>.A<HA 9> does not have a type.
> > > FATAL: Atom .R<THR 2514>.A<HB 10> does not have a type.
> > > FATAL: Atom .R<THR 2514>.A<HG1 11> does not have a type.
> > > FATAL: Atom .R<THR 2514>.A<HG21 12> does not have a type.
> > > FATAL: Atom .R<THR 2514>.A<HG22 13> does not have a type.
> > > FATAL: Atom .R<THR 2514>.A<HG23 14> does not have a type.
> > > FATAL: Atom .R<LYS 2515>.A<N 1> does not have a type.
> > > FATAL: Atom .R<LYS 2515>.A<CA 2> does not have a type.
> > > FATAL: Atom .R<LYS 2515>.A<C 3> does not have a type.
> > > FATAL: Atom .R<LYS 2515>.A<O 4> does not have a type.
> > > FATAL: Atom .R<LYS 2515>.A<CB 5> does not have a type.
> > > FATAL: Atom .R<LYS 2515>.A<CG 6> does not have a type.
> > > FATAL: Atom .R<LYS 2515>.A<CD 7> does not have a type.
> > > FATAL: Atom .R<LYS 2515>.A<CE 8> does not have a type.
> > > FATAL: Atom .R<LYS 2515>.A<NZ 9> does not have a type.
> > > FATAL: Atom .R<LYS 2515>.A<H 10> does not have a type.
> > > FATAL: Atom .R<LYS 2515>.A<HA 11> does not have a type.
> > > FATAL: Atom .R<LYS 2515>.A<HB2 12> does not have a type.
> > > FATAL: Atom .R<LYS 2515>.A<HB3 13> does not have a type.
> > > FATAL: Atom .R<LYS 2515>.A<HG2 14> does not have a type.
> > > FATAL: Atom .R<LYS 2515>.A<HG3 15> does not have a type.
> > > FATAL: Atom .R<LYS 2515>.A<HD2 16> does not have a type.
> > > FATAL: Atom .R<LYS 2515>.A<HD3 17> does not have a type.
> > > FATAL: Atom .R<LYS 2515>.A<HE2 18> does not have a type.
> > > FATAL: Atom .R<LYS 2515>.A<HE3 19> does not have a type.
> > > FATAL: Atom .R<LYS 2515>.A<HZ1 20> does not have a type.
> > > FATAL: Atom .R<LYS 2515>.A<HZ2 21> does not have a type.
> > > FATAL: Atom .R<LYS 2515>.A<HZ3 22> does not have a type.
> > > FATAL: Atom .R<ARG 2516>.A<N 1> does not have a type.
> > > FATAL: Atom .R<ARG 2516>.A<CA 2> does not have a type.
> > > FATAL: Atom .R<ARG 2516>.A<C 3> does not have a type.
> > > FATAL: Atom .R<ARG 2516>.A<O 4> does not have a type.
> > > FATAL: Atom .R<ARG 2516>.A<CB 5> does not have a type.
> > > FATAL: Atom .R<ARG 2516>.A<CG 6> does not have a type.
> > > FATAL: Atom .R<ARG 2516>.A<CD 7> does not have a type.
> > > FATAL: Atom .R<ARG 2516>.A<NE 8> does not have a type.
> > > FATAL: Atom .R<ARG 2516>.A<CZ 9> does not have a type.
> > > FATAL: Atom .R<ARG 2516>.A<NH1 10> does not have a type.
> > > FATAL: Atom .R<ARG 2516>.A<NH2 11> does not have a type.
> > > FATAL: Atom .R<ARG 2516>.A<H 12> does not have a type.
> > > FATAL: Atom .R<ARG 2516>.A<HA 13> does not have a type.
> > > FATAL: Atom .R<ARG 2516>.A<HB2 14> does not have a type.
> > > FATAL: Atom .R<ARG 2516>.A<HB3 15> does not have a type.
> > > FATAL: Atom .R<ARG 2516>.A<HG2 16> does not have a type.
> > > FATAL: Atom .R<ARG 2516>.A<HG3 17> does not have a type.
> > > FATAL: Atom .R<ARG 2516>.A<HD2 18> does not have a type.
> > > FATAL: Atom .R<ARG 2516>.A<HD3 19> does not have a type.
> > > FATAL: Atom .R<ARG 2516>.A<HE 20> does not have a type.
> > > FATAL: Atom .R<ARG 2516>.A<HH11 21> does not have a type.
> > > FATAL: Atom .R<ARG 2516>.A<HH12 22> does not have a type.
> > > FATAL: Atom .R<ARG 2516>.A<HH21 23> does not have a type.
> > > FATAL: Atom .R<ARG 2516>.A<HH22 24> does not have a type.
> > > FATAL: Atom .R<LYS 2517>.A<N 1> does not have a type.
> > > FATAL: Atom .R<LYS 2517>.A<CA 2> does not have a type.
> > > FATAL: Atom .R<LYS 2517>.A<C 3> does not have a type.
> > > FATAL: Atom .R<LYS 2517>.A<O 4> does not have a type.
> > > FATAL: Atom .R<LYS 2517>.A<CB 5> does not have a type.
> > > FATAL: Atom .R<LYS 2517>.A<CG 6> does not have a type.
> > > FATAL: Atom .R<LYS 2517>.A<CD 7> does not have a type.
> > > FATAL: Atom .R<LYS 2517>.A<CE 8> does not have a type.
> > > FATAL: Atom .R<LYS 2517>.A<NZ 9> does not have a type.
> > > FATAL: Atom .R<LYS 2517>.A<H 10> does not have a type.
> > > FATAL: Atom .R<LYS 2517>.A<HA 11> does not have a type.
> > > FATAL: Atom .R<LYS 2517>.A<HB2 12> does not have a type.
> > > FATAL: Atom .R<LYS 2517>.A<HB3 13> does not have a type.
> > > FATAL: Atom .R<LYS 2517>.A<HG2 14> does not have a type.
> > > FATAL: Atom .R<LYS 2517>.A<HG3 15> does not have a type.
> > > FATAL: Atom .R<LYS 2517>.A<HD2 16> does not have a type.
> > > FATAL: Atom .R<LYS 2517>.A<HD3 17> does not have a type.
> > > FATAL: Atom .R<LYS 2517>.A<HE2 18> does not have a type.
> > > FATAL: Atom .R<LYS 2517>.A<HE3 19> does not have a type.
> > > FATAL: Atom .R<LYS 2517>.A<HZ1 20> does not have a type.
> > > FATAL: Atom .R<LYS 2517>.A<HZ2 21> does not have a type.
> > > FATAL: Atom .R<LYS 2517>.A<HZ3 22> does not have a type.
> > > FATAL: Atom .R<LEU 2518>.A<N 1> does not have a type.
> > > FATAL: Atom .R<LEU 2518>.A<CA 2> does not have a type.
> > > FATAL: Atom .R<LEU 2518>.A<C 3> does not have a type.
> > > FATAL: Atom .R<LEU 2518>.A<O 4> does not have a type.
> > > FATAL: Atom .R<LEU 2518>.A<CB 5> does not have a type.
> > > FATAL: Atom .R<LEU 2518>.A<CG 6> does not have a type.
> > > FATAL: Atom .R<LEU 2518>.A<CD1 7> does not have a type.
> > > FATAL: Atom .R<LEU 2518>.A<CD2 8> does not have a type.
> > > FATAL: Atom .R<LEU 2518>.A<H 9> does not have a type.
> > > FATAL: Atom .R<LEU 2518>.A<HA 10> does not have a type.
> > > FATAL: Atom .R<LEU 2518>.A<HB2 11> does not have a type.
> > > FATAL: Atom .R<LEU 2518>.A<HB3 12> does not have a type.
> > > FATAL: Atom .R<LEU 2518>.A<HG 13> does not have a type.
> > > FATAL: Atom .R<LEU 2518>.A<HD11 14> does not have a type.
> > > FATAL: Atom .R<LEU 2518>.A<HD12 15> does not have a type.
> > > FATAL: Atom .R<LEU 2518>.A<HD13 16> does not have a type.
> > > FATAL: Atom .R<LEU 2518>.A<HD21 17> does not have a type.
> > > FATAL: Atom .R<LEU 2518>.A<HD22 18> does not have a type.
> > > FATAL: Atom .R<LEU 2518>.A<HD23 19> does not have a type.
> > > FATAL: Atom .R<ALA 2519>.A<N 1> does not have a type.
> > > FATAL: Atom .R<ALA 2519>.A<CA 2> does not have a type.
> > > FATAL: Atom .R<ALA 2519>.A<C 3> does not have a type.
> > > FATAL: Atom .R<ALA 2519>.A<O 4> does not have a type.
> > > FATAL: Atom .R<ALA 2519>.A<CB 5> does not have a type.
> > > FATAL: Atom .R<ALA 2519>.A<H 6> does not have a type.
> > > FATAL: Atom .R<ALA 2519>.A<HA 7> does not have a type.
> > > FATAL: Atom .R<ALA 2519>.A<HB1 8> does not have a type.
> > > FATAL: Atom .R<ALA 2519>.A<HB2 9> does not have a type.
> > > FATAL: Atom .R<ALA 2519>.A<HB3 10> does not have a type.
> > > FATAL: Atom .R<SER 2520>.A<N 1> does not have a type.
> > > FATAL: Atom .R<SER 2520>.A<CA 2> does not have a type.
> > > FATAL: Atom .R<SER 2520>.A<C 3> does not have a type.
> > > FATAL: Atom .R<SER 2520>.A<O 4> does not have a type.
> > > FATAL: Atom .R<SER 2520>.A<CB 5> does not have a type.
> > > FATAL: Atom .R<SER 2520>.A<OG 6> does not have a type.
> > > FATAL: Atom .R<SER 2520>.A<H 7> does not have a type.
> > > FATAL: Atom .R<SER 2520>.A<HA 8> does not have a type.
> > > FATAL: Atom .R<SER 2520>.A<HB2 9> does not have a type.
> > > FATAL: Atom .R<SER 2520>.A<HB3 10> does not have a type.
> > > FATAL: Atom .R<SER 2520>.A<HG 11> does not have a type.
> > > FATAL: Atom .R<ALA 2521>.A<N 1> does not have a type.
> > > FATAL: Atom .R<ALA 2521>.A<CA 2> does not have a type.
> > > FATAL: Atom .R<ALA 2521>.A<C 3> does not have a type.
> > > FATAL: Atom .R<ALA 2521>.A<O 4> does not have a type.
> > > FATAL: Atom .R<ALA 2521>.A<CB 5> does not have a type.
> > > FATAL: Atom .R<ALA 2521>.A<H 6> does not have a type.
> > > FATAL: Atom .R<ALA 2521>.A<HA 7> does not have a type.
> > > FATAL: Atom .R<ALA 2521>.A<HB1 8> does not have a type.
> > > FATAL: Atom .R<ALA 2521>.A<HB2 9> does not have a type.
> > > FATAL: Atom .R<ALA 2521>.A<HB3 10> does not have a type.
> > > FATAL: Atom .R<VAL 2522>.A<N 1> does not have a type.
> > > FATAL: Atom .R<VAL 2522>.A<CA 2> does not have a type.
> > > FATAL: Atom .R<VAL 2522>.A<C 3> does not have a type.
> > > FATAL: Atom .R<VAL 2522>.A<O 4> does not have a type.
> > > FATAL: Atom .R<VAL 2522>.A<CB 5> does not have a type.
> > > FATAL: Atom .R<VAL 2522>.A<CG1 6> does not have a type.
> > > FATAL: Atom .R<VAL 2522>.A<CG2 7> does not have a type.
> > > FATAL: Atom .R<VAL 2522>.A<OXT 8> does not have a type.
> > > FATAL: Atom .R<VAL 2522>.A<H 9> does not have a type.
> > > FATAL: Atom .R<VAL 2522>.A<HA 10> does not have a type.
> > > FATAL: Atom .R<VAL 2522>.A<HB 11> does not have a type.
> > > FATAL: Atom .R<VAL 2522>.A<HG11 12> does not have a type.
> > > FATAL: Atom .R<VAL 2522>.A<HG12 13> does not have a type.
> > > FATAL: Atom .R<VAL 2522>.A<HG13 14> does not have a type.
> > > FATAL: Atom .R<VAL 2522>.A<HG21 15> does not have a type.
> > > FATAL: Atom .R<VAL 2522>.A<HG22 16> does not have a type.
> > > FATAL: Atom .R<VAL 2522>.A<HG23 17> does not have a type.
> > > Failed to generate parameters
> > > Parameter file was not saved.
> > > Regards,
> > > Vani Panguluri
> > > _______________________________________________
> > > 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
> >
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Feb 02 2011 - 12:00:04 PST
