[gmx-users] Cytochrom C
Dariush Mohammadyani
d.mohammadyani at gmail.com
Tue Jan 10 21:40:42 CET 2012
Does anybody know where can I find [ HIS ] parameters?
Thanks,
Dariush
On Sat, Jan 7, 2012 at 3:58 AM, Dariush Mohammadyani <
d.mohammadyani at gmail.com> wrote:
> Dear Peter and Krzyszto,
>
> Thank you. I am following your comments. If I get any problem I will come
> back.
>
>
>
>
> On Fri, Jan 6, 2012 at 2:18 PM, Peter C. Lai <pcl at uab.edu> wrote:
>
>> He must be using an older version of Gromacs. 4.5.4 and lower don't have
>> ACE in charmm27.
>>
>> On 2012-01-06 12:59:56PM -0600, Krzysztof Kuczera wrote:
>> > Here is the blocking group from
>> > gromacs-4.5.5/share/top/charmm27.ff/aminoacids.rtp
>> > KK
>> >
>> > [ ACE ]
>> > [ atoms ]
>> > CH3 CT3 -0.270 0
>> > HH31 HA 0.090 1
>> > HH32 HA 0.090 2
>> > HH33 HA 0.090 3
>> > C C 0.510 4
>> > O O -0.510 5
>> > [ bonds ]
>> > C CH3
>> > C +N
>> > CH3 HH31
>> > CH3 HH32
>> > CH3 HH33
>> > O C
>> > [ impropers ]
>> > C CH3 +N O
>> >
>> >
>> > On 1/6/12 12:40 PM, Peter C. Lai wrote:
>> > > Corrected bonds section (sorry been up all night)
>> > >
>> > > [ ACE ]
>> > > [ atoms ]
>> > > CH3 CT3 -0.27 0
>> > > HH31 HA 0.09 1
>> > > HH32 HA 0.09 2
>> > > HH33 HA 0.09 3
>> > > C C 0.51 4
>> > > O O -0.51 5
>> > > [ bonds ]
>> > > CH3 HH31
>> > > CH3 HH32
>> > > CH3 HH33
>> > > CH3 C
>> > > C O
>> > >
>> > > Surprisingly, an .hdb entry for ACE exists so you don't need to
>> create one.
>> > > (and the .hdb entry uses HH3 as the base hydrogen name in ACE)
>> > >
>> > >>
>> > >> On 2012-01-06 12:23:49PM -0600, Peter C. Lai wrote:
>> > >>> Gromos96 53A6 has it.
>> > >>>
>> > >>> On 2012-01-06 01:18:38PM -0500, Dariush Mohammadyani wrote:
>> > >>>> I tried charmm27 too.
>> > >>>>
>> > >>>> Error:
>> > >>>> Residue 'ACE' not found in residue topology database
>> > >>>>
>> > >>>> I tried all forcefield in the list provided by "pdb2gmx", but non
>> of them
>> > >>>> works.
>> > >>>>
>> > >>>> Dariush
>> > >>>>
>> > >>>>
>> > >>>> On Thu, Jan 5, 2012 at 1:42 PM, Robert Hamers<rjhamers at wisc.edu>
>> wrote:
>> > >>>>
>> > >>>>> HEME is in the charmm27 force field.
>> > >>>>> bob h.
>> > >>>>>
>> > >>>>>
>> > >>>>>
>> > >>>>>
>> > >>>>> On 1/5/2012 12:00 PM, Dariush Mohammadyani wrote:
>> > >>>>>
>> > >>>>> Yes, I have PDB file (1HRC.pdb). However, when I try to use
>> "pdb2gmx" I
>> > >>>>> get this error:
>> > >>>>>
>> > >>>>> Residue 'HEM' not found in residue topology database
>> > >>>>>
>> > >>>>> and HEM is Iron ion inside this protein. I do not know which
>> forcefield is
>> > >>>>> proper to use. I also tried MARTINI force field according their
>> website; I
>> > >>>>> used martinize.py script; Again I got error.
>> > >>>>>
>> > >>>>> Regards,
>> > >>>>> Dariush
>> > >>>>>
>> > >>>>>
>> > >>>>>
>> > >>>>>
>> > >>>>> On Thu, Jan 5, 2012 at 11:51 AM, Justin A. Lemkul<jalemkul at vt.edu>
>> wrote:
>> > >>>>>
>> > >>>>>>
>> > >>>>>> Dariush Mohammadyani wrote:
>> > >>>>>>
>> > >>>>>>> Hi all,
>> > >>>>>>>
>> > >>>>>>> Has anybody made initial configuration for Cytochrom C? Can it
>> be shared
>> > >>>>>>> with me?
>> > >>>>>>>
>> > >>>>>>>
>> > >>>>>> There are several in the PDB.
>> > >>>>>>
>> > >>>>>> -Justin
>> > >>>>>>
>> > >>>>>> --
>> > >>>>>> ========================================
>> > >>>>>>
>> > >>>>>> Justin A. Lemkul
>> > >>>>>> Ph.D. Candidate
>> > >>>>>> ICTAS Doctoral Scholar
>> > >>>>>> MILES-IGERT Trainee
>> > >>>>>> Department of Biochemistry
>> > >>>>>> Virginia Tech
>> > >>>>>> Blacksburg, VA
>> > >>>>>> jalemkul[at]vt.edu | (540) 231-9080
>> > >>>>>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>> > >>>>>>
>> > >>>>>> ========================================
>> > >>>>>>
>> > >>>>>> --
>> > >>>>>> gmx-users mailing list gmx-users at gromacs.org
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>> > >>>>>>
>> > >>>>>
>> > >>>>>
>> > >>>>>
>> > >>>>>
>> > >>>>>
>> > >>>>>
>> > >>>>> --
>> > >>>>> Robert J. Hamers
>> > >>>>> Wisconsin Distinguished Professor
>> > >>>>> Univ. of Wisconsin-Madison
>> > >>>>> 1101 University Avenue
>> > >>>>> Madison, WI 53706
>> > >>>>> Ph: 608-262-6371
>> > >>>>> Web: http://hamers.chem.wisc.edu
>> > >>>>>
>> > >>>>>
>> > >>>>
>> > >>>> --
>> > >>>> Kind Regards,
>> > >>>> Dariush Mohammadyani
>> > >>>> Department of Structural Biology
>> > >>>> University of Pittsburgh School of Medicine
>> > >>>> Biomedical Science Tower 3
>> > >>>> 3501 Fifth Avenue
>> > >>>> Pittsburgh, PA 15261
>> > >>>> USA
>> > >>>> --
>> > >>>> gmx-users mailing list gmx-users at gromacs.org
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>> > >>>
>> > >>> --
>> > >>> ==================================================================
>> > >>> Peter C. Lai | University of Alabama-Birmingham
>> > >>> Programmer/Analyst | KAUL 752A
>> > >>> Genetics, Div. of Research | 705 South 20th Street
>> > >>> pcl at uab.edu | Birmingham AL 35294-4461
>> > >>> (205) 690-0808 |
>> > >>> ==================================================================
>> > >>>
>> > >>> --
>> > >>> gmx-users mailing list gmx-users at gromacs.org
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>> > >> --
>> > >> ==================================================================
>> > >> Peter C. Lai | University of Alabama-Birmingham
>> > >> Programmer/Analyst | KAUL 752A
>> > >> Genetics, Div. of Research | 705 South 20th Street
>> > >> pcl at uab.edu | Birmingham AL 35294-4461
>> > >> (205) 690-0808 |
>> > >> ==================================================================
>> > >>
>> > >> --
>> > >> gmx-users mailing list gmx-users at gromacs.org
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>> >
>> > --
>> > Krzysztof Kuczera
>> > Professor
>> > Departments of Chemistry and Molecular Biosciences
>> > The University of Kansas
>> > 2010 Malott Hall
>> > Lawrence, KS 66045
>> > Tel: 785-864-5060 Fax: 785-864-5396 email: kkuczera at ku.edu
>> > http://oolung.chem.ku.edu/~kuczera/home.html
>> >
>> >
>> >
>> > --
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>> --
>> ==================================================================
>> Peter C. Lai | University of Alabama-Birmingham
>> Programmer/Analyst | KAUL 752A
>> Genetics, Div. of Research | 705 South 20th Street
>> pcl at uab.edu | Birmingham AL 35294-4461
>> (205) 690-0808 |
>> ==================================================================
>>
>> --
>> gmx-users mailing list gmx-users at gromacs.org
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>
>
>
> --
> Kind Regards,
> Dariush Mohammadyani
> Department of Structural Biology
> University of Pittsburgh School of Medicine
> Biomedical Science Tower 3
> 3501 Fifth Avenue
> Pittsburgh, PA 15261
> USA
>
>
--
Kind Regards,
Dariush Mohammadyani
Department of Structural Biology
University of Pittsburgh School of Medicine
Biomedical Science Tower 3
3501 Fifth Avenue
Pittsburgh, PA 15261
USA
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