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<rjham...@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<jalem...@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@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-requ...@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@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-requ...@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 > >>> p...@uab.edu | Birmingham AL 35294-4461 > >>> (205) 690-0808 | > >>> ================================================================== > >>> > >>> -- > >>> gmx-users mailing list gmx-users@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-requ...@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 > >> p...@uab.edu | Birmingham AL 35294-4461 > >> (205) 690-0808 | > >> ================================================================== > >> > >> -- > >> gmx-users mailing list gmx-users@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-requ...@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: kkucz...@ku.edu > http://oolung.chem.ku.edu/~kuczera/home.html > > > > -- > gmx-users mailing list gmx-users@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-requ...@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 p...@uab.edu | Birmingham AL 35294-4461 (205) 690-0808 | ================================================================== -- gmx-users mailing list gmx-users@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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
