[gmx-users] Cytochrom C
Dariush Mohammadyani
d.mohammadyani at gmail.com
Tue Jan 17 16:27:47 CET 2012
According your help and "pdb2gmx -his -missing" I could create input files.
Also I used grompp without error. However, for mdrun I got this error:
*Function type CMAP Dih. not implemented in ip_pert*
How can I figure it out?
Thanks,
Dariush
On Tue, Jan 10, 2012 at 4:37 PM, Krzysztof Kuczera <kkuczera at ku.edu> wrote:
> 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> 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 <%28540%29%20231-9080>
> > >>>>>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> > >>>>>>
> > >>>>>> ========================================
> > >>>>>>
> > >>>>>> --
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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
> > >>>> --
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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 <%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 | Birmingham AL 35294-4461
> > >> (205) 690-0808 <%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 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 <%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.eduhttp://oolung.chem.ku.edu/~kuczera/home.html
>
>
> --
> gmx-users mailing list gmx-users at gromacs.org
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