- Contemporary messages sorted: [ by date ] [ by thread ] [ by subject ] [ by author ] [ by messages with attachments ]

From: peker milas <pekermilas.gmail.com>

Date: Wed, 2 Feb 2011 14:58:01 -0500

Dear Vani,

For me it was almost always good to take a look at the amber tutorials

in amber's web page. Therefore i will advise you to do the same. There

in first basic tutorial (see

"http://ambermd.org/tutorials/basic/tutorial1/section2.htm") you will

notice you need to edit your residue or molecule. When you choose all

the atoms and say edit a table like object will show up. There you

will see charges,types,names etc... for each atom. That is being said,

in amber there are specific atom types for example when you say Carbon

you need to tell amber whether it is a Carbon with sp3 hybradization

or something else. This is the issue you need to consider.

As Jason already stated, before you load your molecule/residue you

need to load or tell amber which force field you want to use. In fact

this is also being explained more in above tutorial. If those don't

work, just let people know again...

best

peker

On Wed, Feb 2, 2011 at 2:50 PM, Jason Swails <jason.swails.gmail.com> wrote:

*> 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
*

*>
*

_______________________________________________

AMBER mailing list

AMBER.ambermd.org

http://lists.ambermd.org/mailman/listinfo/amber

Received on Wed Feb 02 2011 - 12:00:05 PST

Date: Wed, 2 Feb 2011 14:58:01 -0500

Dear Vani,

For me it was almost always good to take a look at the amber tutorials

in amber's web page. Therefore i will advise you to do the same. There

in first basic tutorial (see

"http://ambermd.org/tutorials/basic/tutorial1/section2.htm") you will

notice you need to edit your residue or molecule. When you choose all

the atoms and say edit a table like object will show up. There you

will see charges,types,names etc... for each atom. That is being said,

in amber there are specific atom types for example when you say Carbon

you need to tell amber whether it is a Carbon with sp3 hybradization

or something else. This is the issue you need to consider.

As Jason already stated, before you load your molecule/residue you

need to load or tell amber which force field you want to use. In fact

this is also being explained more in above tutorial. If those don't

work, just let people know again...

best

peker

On Wed, Feb 2, 2011 at 2:50 PM, Jason Swails <jason.swails.gmail.com> wrote:

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Received on Wed Feb 02 2011 - 12:00:05 PST

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