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 <kkucz...@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.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 <%28540%29%20231-9080> > > >>>>>> 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 <%28205%29%20690-0808> | > > >>> ================================================================== > > >>> > > >>> -- > > >>> 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 <%28205%29%20690-0808> | > > >> ================================================================== > > >> > > >> -- > > >> 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 <%28205%29%20690-0808> | > ================================================================== > > -- > 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 > > > > > > -- > 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@ku.eduhttp://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 >
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