[gmx-users] Cytochrom C
Peter C. Lai
pcl at uab.edu
Fri Jan 6 20:18:34 CET 2012
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
> >>>>>> http://lists.gromacs.org/mailman/listinfo/gmx-users
> >>>>>> Please search the archive at
> >>>>>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> >>>>>> Please don't post (un)subscribe requests to the list. Use the www
> >>>>>> interface or send it to gmx-users-request at gromacs.org.
> >>>>>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >>>>>>
> >>>>>
> >>>>>
> >>>>>
> >>>>>
> >>>>>
> >>>>>
> >>>>> --
> >>>>> 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
> >>>> http://lists.gromacs.org/mailman/listinfo/gmx-users
> >>>> Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> >>>> Please don't post (un)subscribe requests to the list. Use the
> >>>> www interface or send it to gmx-users-request at gromacs.org.
> >>>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >>>
> >>> --
> >>> ==================================================================
> >>> 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
> >>> http://lists.gromacs.org/mailman/listinfo/gmx-users
> >>> Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> >>> Please don't post (un)subscribe requests to the list. Use the
> >>> www interface or send it to gmx-users-request at gromacs.org.
> >>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >> --
> >> ==================================================================
> >> 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
> >> http://lists.gromacs.org/mailman/listinfo/gmx-users
> >> Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> >> Please don't post (un)subscribe requests to the list. Use the
> >> www interface or send it to gmx-users-request at gromacs.org.
> >> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
>
> --
> 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
>
>
>
> --
> gmx-users mailing list gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
--
==================================================================
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 |
==================================================================
More information about the gromacs.org_gmx-users
mailing list