Re: [gmx-users] generation of gro file
Dear Justin Thanks a lot. will definitely do it. warm regards On Sun, Aug 18, 2013 at 10:53 AM, Musharaf Ali skmali...@gmail.com wrote: Dear Justin Again thanks. Actually the problem arises in the running of pdb2gmx of pdb file of crown ether. I have generated the pdb file from xyz coordinates using openbabel. The pdb file looks like below. COMPND D:\data-structure\18c6.xyz AUTHOR GENERATED BY OPEN BABEL 2.3.2 HETATM 1 O LIG 1 0.000 0.000 0.000 1.00 0.00 O HETATM 2 C LIG 1 0.000 0.000 1.400 1.00 0.00 C HETATM 3 C LIG 1 1.367 0.000 1.883 1.00 0.00 C HETATM 4 H LIG 1 -0.513 0.889 1.763 1.00 0.00 H HETATM 5 H LIG 1 -0.513 -0.889 1.763 1.00 0.00 H HETATM 6 H LIG 1 1.367 0.000 2.972 1.00 0.00 H HETATM 7 O LIG 1 2.027 -1.143 1.417 1.00 0.00 O HETATM 8 H LIG 1 1.880 0.889 1.520 1.00 0.00 H HETATM 9 C LIG 1 3.347 -1.143 1.883 1.00 0.00 C HETATM 10 C LIG 1 4.031 -2.327 1.400 1.00 0.00 C HETATM 11 H LIG 1 3.860 -0.254 1.520 1.00 0.00 H HETATM 12 H LIG 1 3.347 -1.143 2.972 1.00 0.00 H HETATM 13 H LIG 1 5.057 -2.327 1.763 1.00 0.00 H HETATM 14 H LIG 1 3.517 -3.216 1.763 1.00 0.00 H HETATM 15 O LIG 1 4.031 -2.327 -0.000 1.00 0.00 O HETATM 16 C LIG 1 4.690 -3.470 -0.467 1.00 0.00 C HETATM 17 C LIG 1 4.690 -3.470 -1.917 1.00 0.00 C HETATM 18 H LIG 1 5.717 -3.470 -0.104 1.00 0.00 H HETATM 19 H LIG 1 4.177 -4.359 -0.104 1.00 0.00 H HETATM 20 H LIG 1 5.204 -4.359 -2.280 1.00 0.00 H HETATM 21 O LIG 1 3.371 -3.470 -2.383 1.00 0.00 O HETATM 22 H LIG 1 5.204 -2.581 -2.280 1.00 0.00 H HETATM 23 C LIG 1 3.371 -3.470 -3.783 1.00 0.00 C HETATM 24 C LIG 1 2.003 -3.470 -4.267 1.00 0.00 C HETATM 25 H LIG 1 3.884 -2.581 -4.146 1.00 0.00 H HETATM 26 H LIG 1 3.884 -4.359 -4.146 1.00 0.00 H HETATM 27 H LIG 1 2.003 -3.470 -5.356 1.00 0.00 H HETATM 28 H LIG 1 1.490 -4.359 -3.904 1.00 0.00 H HETATM 29 O LIG 1 1.343 -2.327 -3.800 1.00 0.00 O HETATM 30 C LIG 1 0.024 -2.327 -4.267 1.00 0.00 C HETATM 31 C LIG 1 -0.660 -1.143 -3.783 1.00 0.00 C HETATM 32 H LIG 1 0.024 -2.327 -5.356 1.00 0.00 H HETATM 33 H LIG 1 -0.490 -3.216 -3.904 1.00 0.00 H HETATM 34 H LIG 1 -1.687 -1.143 -4.146 1.00 0.00 H HETATM 35 O LIG 1 -0.660 -1.143 -2.383 1.00 0.00 O HETATM 36 H LIG 1 -0.147 -0.254 -4.146 1.00 0.00 H HETATM 37 C LIG 1 -1.320 0.000 -1.917 1.00 0.00 C HETATM 38 C LIG 1 -1.320 0.000 -0.467 1.00 0.00 C HETATM 39 H LIG 1 -0.807 0.889 -2.280 1.00 0.00 H HETATM 40 H LIG 1 -2.347 0.000 -2.280 1.00 0.00 H HETATM 41 H LIG 1 -1.833 0.889 -0.104 1.00 0.00 H HETATM 42 H LIG 1 -1.833 -0.889 -0.104 1.00 0.00 H CONECT 1 38 2 CONECT 2 1 5 4 3 CONECT 2 CONECT 3 2 7 8 6 CONECT 3 CONECT 4 2 CONECT 5 2 CONECT 6 3 CONECT 7 9 3 CONECT 8 3 CONECT 9 10 7 11 12 CONECT 9 CONECT 10 15 13 14 9 CONECT 10 CONECT 11 9 CONECT 12 9 CONECT 13 10 CONECT 14 10 CONECT 15 16 10 CONECT 16 17 18 19 15 CONECT 16 CONECT 17 21 22 20 16 CONECT 17 CONECT 18 16 CONECT 19 16 CONECT 20 17 CONECT 21 23 17 CONECT 22 17 CONECT 23 24 26 25 21 CONECT 23 CONECT 24 27 28 29 23 CONECT 24 CONECT 25 23 CONECT 26 23 CONECT 27 24 CONECT 28 24 CONECT 29 24 30 CONECT 30 32 33 29 31 CONECT 30 CONECT 31 30 36 34 35 CONECT 31 CONECT 32 30 CONECT 33 30 CONECT 34 31 CONECT 35 31 37 CONECT 36 31 CONECT 37 35 39 40 38 CONECT 37 CONECT 38 37 41 42 1 CONECT 38 CONECT 39 37 CONECT 40 37 CONECT 41 38 CONECT 42 38 MASTER 0 0 0 0 0 0 0 0 42 0 42 0 END Now my query is whether this pdb format i can directly used for pdb2gmx or i have to change the LIG temr to OPLS force field term. If you can guide here then the problem will be sorted out. warm regards SMA On Sat, Aug 17, 2013 at 8:33 PM, Justin Lemkul jalem...@vt.edu wrote: On 8/17/13 10:58 AM, Musharaf Ali wrote: Thank You Justin But you mean to say that even XYZ coordinates like below format (18-crown-6) can be directly used in Gromacs. I don't know. I seem to recall some discussion about .xyz files some time ago, but I forget the outcome. My point was that most new users think that .gro files are absolutely required, which is not true. Numerous file formats are accepted. Check the manual and Gromacs website. You may need to convert to another format, but it doesn't necessarily have to be .gro. -Justin O 0.00 0.00 0.00 C 0.00 0.00 1.40 C 1.367075 0.00 1.883328 H -0.513360 0.889165 1.763000 H -0.513360 -0.889165 1.763000 H 1.367079 0.00 2.972328 O 2.027040 -1.143095 1.416659 H 1.880433 0.889165 1.520326 C 3.346974 -1.143095 1.883320 C 4.030509 -2.327015 1.399984 H 3.860332 -0.253930 1.520318 H 3.346978 -1.143095 2.972320 H 5.057229 -2.327015 1.762981 H 3.517151 -3.216180 1.762986 O 4.030503 -2.327015 -0.16 C 4.690468 -3.470110 -0.466685 C 4.690462 -3.470110 -1.916685 H 5.717188 -3.470110 -0.103689 H 4.177110 -4.359275 -0.103683 H 5.203820 -4.359275 -2.279687 O
Re: [gmx-users] generation of gro file
Thank You Justin But you mean to say that even XYZ coordinates like below format (18-crown-6) can be directly used in Gromacs. O 0.00 0.00 0.00 C 0.00 0.00 1.40 C 1.367075 0.00 1.883328 H -0.513360 0.889165 1.763000 H -0.513360 -0.889165 1.763000 H 1.367079 0.00 2.972328 O 2.027040 -1.143095 1.416659 H 1.880433 0.889165 1.520326 C 3.346974 -1.143095 1.883320 C 4.030509 -2.327015 1.399984 H 3.860332 -0.253930 1.520318 H 3.346978 -1.143095 2.972320 H 5.057229 -2.327015 1.762981 H 3.517151 -3.216180 1.762986 O 4.030503 -2.327015 -0.16 C 4.690468 -3.470110 -0.466685 C 4.690462 -3.470110 -1.916685 H 5.717188 -3.470110 -0.103689 H 4.177110 -4.359275 -0.103683 H 5.203820 -4.359275 -2.279687 O 3.370528 -3.470110 -2.383346 H 5.203820 -2.580946 -2.279687 C 3.370522 -3.470110 -3.783346 C 2.003447 -3.470110 -4.266674 H 3.883880 -2.580946 -4.146348 H 3.883880 -4.359275 -4.146348 H 2.003443 -3.470110 -5.355674 H 1.490089 -4.359275 -3.903672 O 1.343483 -2.327015 -3.85 C 0.023548 -2.327015 -4.27 C -0.659986 -1.143095 -3.783331 H 0.023544 -2.327015 -5.355667 H -0.489810 -3.216180 -3.903665 H -1.686707 -1.143095 -4.146327 O -0.659981 -1.143095 -2.383331 H -0.146628 -0.253930 -4.146333 C -1.319945 0.00 -1.916662 C -1.319940 0.00 -0.42 H -0.806587 0.889165 -2.279664 H -2.34 0.00 -2.279658 H -1.833298 0.889165 -0.103660 H -1.833298 -0.889165 -0.103660 On Sat, Aug 17, 2013 at 3:53 PM, Justin Lemkul jalem...@vt.edu wrote: On 8/16/13 10:50 PM, Musharaf Ali wrote: Hi could somebody help how to generate grow file from xyz coordinates specially for crown ether type molecules. The specifications of the .gro format are described here: http://manual.gromacs.org/**online/gro.htmlhttp://manual.gromacs.org/online/gro.html Note that there is no requirement to use .gro files in Gromacs. Most formats will be recognized. Here the xyz coordinates are attached for 18-crown-6. Thank in advance. FYI the mailing list does not accept attachments. -Justin -- ==** Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalemkul@outerbanks.umaryland.**edu jalem...@outerbanks.umaryland.edu | (410) 706-7441 ==** -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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_Listshttp://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-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
Re: [gmx-users] generation of gro file
Dear Justin Again thanks. Actually the problem arises in the running of pdb2gmx of pdb file of crown ether. I have generated the pdb file from xyz coordinates using openbabel. The pdb file looks like below. COMPND D:\data-structure\18c6.xyz AUTHOR GENERATED BY OPEN BABEL 2.3.2 HETATM 1 O LIG 1 0.000 0.000 0.000 1.00 0.00 O HETATM 2 C LIG 1 0.000 0.000 1.400 1.00 0.00 C HETATM 3 C LIG 1 1.367 0.000 1.883 1.00 0.00 C HETATM 4 H LIG 1 -0.513 0.889 1.763 1.00 0.00 H HETATM 5 H LIG 1 -0.513 -0.889 1.763 1.00 0.00 H HETATM 6 H LIG 1 1.367 0.000 2.972 1.00 0.00 H HETATM 7 O LIG 1 2.027 -1.143 1.417 1.00 0.00 O HETATM 8 H LIG 1 1.880 0.889 1.520 1.00 0.00 H HETATM 9 C LIG 1 3.347 -1.143 1.883 1.00 0.00 C HETATM 10 C LIG 1 4.031 -2.327 1.400 1.00 0.00 C HETATM 11 H LIG 1 3.860 -0.254 1.520 1.00 0.00 H HETATM 12 H LIG 1 3.347 -1.143 2.972 1.00 0.00 H HETATM 13 H LIG 1 5.057 -2.327 1.763 1.00 0.00 H HETATM 14 H LIG 1 3.517 -3.216 1.763 1.00 0.00 H HETATM 15 O LIG 1 4.031 -2.327 -0.000 1.00 0.00 O HETATM 16 C LIG 1 4.690 -3.470 -0.467 1.00 0.00 C HETATM 17 C LIG 1 4.690 -3.470 -1.917 1.00 0.00 C HETATM 18 H LIG 1 5.717 -3.470 -0.104 1.00 0.00 H HETATM 19 H LIG 1 4.177 -4.359 -0.104 1.00 0.00 H HETATM 20 H LIG 1 5.204 -4.359 -2.280 1.00 0.00 H HETATM 21 O LIG 1 3.371 -3.470 -2.383 1.00 0.00 O HETATM 22 H LIG 1 5.204 -2.581 -2.280 1.00 0.00 H HETATM 23 C LIG 1 3.371 -3.470 -3.783 1.00 0.00 C HETATM 24 C LIG 1 2.003 -3.470 -4.267 1.00 0.00 C HETATM 25 H LIG 1 3.884 -2.581 -4.146 1.00 0.00 H HETATM 26 H LIG 1 3.884 -4.359 -4.146 1.00 0.00 H HETATM 27 H LIG 1 2.003 -3.470 -5.356 1.00 0.00 H HETATM 28 H LIG 1 1.490 -4.359 -3.904 1.00 0.00 H HETATM 29 O LIG 1 1.343 -2.327 -3.800 1.00 0.00 O HETATM 30 C LIG 1 0.024 -2.327 -4.267 1.00 0.00 C HETATM 31 C LIG 1 -0.660 -1.143 -3.783 1.00 0.00 C HETATM 32 H LIG 1 0.024 -2.327 -5.356 1.00 0.00 H HETATM 33 H LIG 1 -0.490 -3.216 -3.904 1.00 0.00 H HETATM 34 H LIG 1 -1.687 -1.143 -4.146 1.00 0.00 H HETATM 35 O LIG 1 -0.660 -1.143 -2.383 1.00 0.00 O HETATM 36 H LIG 1 -0.147 -0.254 -4.146 1.00 0.00 H HETATM 37 C LIG 1 -1.320 0.000 -1.917 1.00 0.00 C HETATM 38 C LIG 1 -1.320 0.000 -0.467 1.00 0.00 C HETATM 39 H LIG 1 -0.807 0.889 -2.280 1.00 0.00 H HETATM 40 H LIG 1 -2.347 0.000 -2.280 1.00 0.00 H HETATM 41 H LIG 1 -1.833 0.889 -0.104 1.00 0.00 H HETATM 42 H LIG 1 -1.833 -0.889 -0.104 1.00 0.00 H CONECT 1 38 2 CONECT 2 1 5 4 3 CONECT 2 CONECT 3 2 7 8 6 CONECT 3 CONECT 4 2 CONECT 5 2 CONECT 6 3 CONECT 7 9 3 CONECT 8 3 CONECT 9 10 7 11 12 CONECT 9 CONECT 10 15 13 14 9 CONECT 10 CONECT 11 9 CONECT 12 9 CONECT 13 10 CONECT 14 10 CONECT 15 16 10 CONECT 16 17 18 19 15 CONECT 16 CONECT 17 21 22 20 16 CONECT 17 CONECT 18 16 CONECT 19 16 CONECT 20 17 CONECT 21 23 17 CONECT 22 17 CONECT 23 24 26 25 21 CONECT 23 CONECT 24 27 28 29 23 CONECT 24 CONECT 25 23 CONECT 26 23 CONECT 27 24 CONECT 28 24 CONECT 29 24 30 CONECT 30 32 33 29 31 CONECT 30 CONECT 31 30 36 34 35 CONECT 31 CONECT 32 30 CONECT 33 30 CONECT 34 31 CONECT 35 31 37 CONECT 36 31 CONECT 37 35 39 40 38 CONECT 37 CONECT 38 37 41 42 1 CONECT 38 CONECT 39 37 CONECT 40 37 CONECT 41 38 CONECT 42 38 MASTER 0 0 0 0 0 0 0 0 42 0 42 0 END Now my query is whether this pdb format i can directly used for pdb2gmx or i have to change the LIG temr to OPLS force field term. If you can guide here then the problem will be sorted out. warm regards SMA On Sat, Aug 17, 2013 at 8:33 PM, Justin Lemkul jalem...@vt.edu wrote: On 8/17/13 10:58 AM, Musharaf Ali wrote: Thank You Justin But you mean to say that even XYZ coordinates like below format (18-crown-6) can be directly used in Gromacs. I don't know. I seem to recall some discussion about .xyz files some time ago, but I forget the outcome. My point was that most new users think that .gro files are absolutely required, which is not true. Numerous file formats are accepted. Check the manual and Gromacs website. You may need to convert to another format, but it doesn't necessarily have to be .gro. -Justin O 0.00 0.00 0.00 C 0.00 0.00 1.40 C 1.367075 0.00 1.883328 H -0.513360 0.889165 1.763000 H -0.513360 -0.889165 1.763000 H 1.367079 0.00 2.972328 O 2.027040 -1.143095 1.416659 H 1.880433 0.889165 1.520326 C 3.346974 -1.143095 1.883320 C 4.030509 -2.327015 1.399984 H 3.860332 -0.253930 1.520318 H 3.346978 -1.143095 2.972320 H 5.057229 -2.327015 1.762981 H 3.517151 -3.216180 1.762986 O 4.030503 -2.327015 -0.16 C 4.690468 -3.470110 -0.466685 C 4.690462 -3.470110 -1.916685 H 5.717188 -3.470110 -0.103689 H 4.177110 -4.359275 -0.103683 H 5.203820 -4.359275 -2.279687 O 3.370528 -3.470110 -2.383346 H 5.203820 -2.580946 -2.279687 C 3.370522 -3.470110 -3.783346 C 2.003447 -3.470110 -4.266674 H 3.883880 -2.580946 -4.146348 H 3.883880 -4.359275 -4.146348 H 2.003443 -3.470110 -5.355674 H 1.490089 -4.359275
[gmx-users] generation of gro file
Hi could somebody help how to generate grow file from xyz coordinates specially for crown ether type molecules. Here the xyz coordinates are attached for 18-crown-6. Thank in advance. Regards New learner -- gmx-users mailing listgmx-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
