or, as Jason said, in inappropriate force field selected (or not
selected at all)..
On Wed, Feb 2, 2011 at 10:59 PM, Dmitry Nilov <nilovdm.gmail.com> wrote:
> It seems that your problem results from incorrect atom names in input
> pdb (is it pdb?) file.
>
> On Wed, Feb 2, 2011 at 10:33 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
>>
>
>
>
> --
> Dmitry Nilov,
> Faculty of Bioengineering and Bioinformatics,
> Lomonosov Moscow State University
>
--
Dmitry Nilov,
Faculty of Bioengineering and Bioinformatics,
Lomonosov Moscow State University
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Received on Wed Feb 02 2011 - 12:30:06 PST
