Does anybody know where can I find [ HIS ] parameters? Thanks, Dariush
On Sat, Jan 7, 2012 at 3:58 AM, Dariush Mohammadyani < d.mohammady...@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 <p...@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<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 >> > > > > -- > 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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