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 0.000000 0.000000 0.000000 >>> >>> C 0.000000 0.000000 1.400000 >>> >>> C 1.367075 0.000000 1.883328 >>> >>> H -0.513360 0.889165 1.763000 >>> >>> H -0.513360 -0.889165 1.763000 >>> >>> H 1.367079 0.000000 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 -0.000016 >>> >>> 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 -3.800005 >>> >>> C 0.023548 -2.327015 -4.266667 >>> >>> 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 0.000000 -1.916662 >>> >>> C -1.319940 0.000000 -0.466662 >>> >>> H -0.806587 0.889165 -2.279664 >>> >>> H -2.346666 0.000000 -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.html<http://manual.gromacs.org/**online/gro.html> >>>> <http://manual.**gromacs.org/online/gro.html<http://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 <jalemkul@outerbanks.** >>>> umaryland.edu <jalem...@outerbanks.umaryland.edu>> | >>>> (410) 706-7441 >>>> >>>> ==============================****==================== >>>> >>>> -- >>>> gmx-users mailing list gmx-users@gromacs.org >>>> http://lists.gromacs.org/****mailman/listinfo/gmx-users<http://lists.gromacs.org/**mailman/listinfo/gmx-users> >>>> <htt**p://lists.gromacs.org/mailman/**listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> >>>> > >>>> * Please search the archive at http://www.gromacs.org/** >>>> Support/Mailing_Lists/Search<h**ttp://www.gromacs.org/Support/** >>>> Mailing_Lists/Search<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<http://www.gromacs.org/**Support/Mailing_Lists> >>>> <http://**www.gromacs.org/Support/**Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> >>>> > >>>> >>>> >> -- >> ==============================**==================== >> >> 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 list gmx-users@gromacs.org >> http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> >> * Please search the archive at http://www.gromacs.org/** >> Support/Mailing_Lists/Search<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<http://www.gromacs.org/Support/Mailing_Lists> >> > > -- 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
