[gmx-users] Cytochrom C
Krzysztof Kuczera
kkuczera at ku.edu
Tue Jan 10 22:37:02 CET 2012
Hi Dariush
If you are using the CHARMM27 force field, then all topology and parameters
are in your share/top/charmm27.ff directory
The defined molecules are listed in aminoacids.rtp and force field
parameters in
numerous other files. CHARMM does not use 'HIS' for histidine, but has
HSD, HSE and HSP for the isomers with hydrogen at ND1, NE2 and both.
You can either set these isomers by hand - by editing your PDB file or
use the
'pdb2gmx -his' option for interactive definition.
The bonus of keeping 'HIS' names and interactive setup is that bonds to heme
iron will be generated based on the 'specbond.dat' entries, if HIS NE2
nitrogens are close enough to the FE.
Krzysztof
On 1/10/12 2:40 PM, Dariush Mohammadyani wrote:
> 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 <mailto: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
> <mailto: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 <tel:2012-01-06%2012>: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 <tel:2012-01-06%2012>:23:49PM -0600,
> Peter C. Lai wrote:
> > >>> Gromos96 53A6 has it.
> > >>>
> > >>> On 2012-01-06 01 <tel:2012-01-06%2001>: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 <mailto: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 <mailto: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 <http://vt.edu> | (540) 231-9080
> <tel:%28540%29%20231-9080>
> > >>>>>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> > >>>>>>
> > >>>>>> ========================================
> > >>>>>>
> > >>>>>> --
> > >>>>>> gmx-users mailing list gmx-users at gromacs.org
> <mailto: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 <tel: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
> > >>>> --
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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 <mailto:pcl at uab.edu> |
> Birmingham AL 35294-4461
> > >>> (205) 690-0808 <tel:%28205%29%20690-0808> |
> > >>>
> ==================================================================
> > >>>
> > >>> --
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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 <mailto:pcl at uab.edu> |
> Birmingham AL 35294-4461
> > >> (205) 690-0808 <tel:%28205%29%20690-0808> |
> > >>
> ==================================================================
> > >>
> > >> --
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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 <tel:785-864-5060> Fax: 785-864-5396
> <tel:785-864-5396> email: kkuczera at ku.edu <mailto:kkuczera at ku.edu>
> > http://oolung.chem.ku.edu/~kuczera/home.html
> <http://oolung.chem.ku.edu/%7Ekuczera/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 <mailto:pcl at uab.edu> |
> Birmingham AL 35294-4461
> (205) 690-0808 <tel:%28205%29%20690-0808> |
> ==================================================================
>
> --
> 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
>
>
>
--
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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