[gmx-users] itp problem
Hello: I am trying to restrain part of my protein. First I generate a index file by make_ndx. Then I use genrest for this purpose like: genres -f npt.gro -o helix -n -fc 400 after that I change the following in the topol.top file, like: ; Include Position restraint file #ifdef POSRES #include helix.itp #endif when I run grompp, it claimed following warnings: WARNING 1 [file helix.itp, line 1]: Too few parameters on line (source file /home/albert/install/source/gromacs-4.6.3/src/kernel/toppush.c, line 1756) here is my helix.itp: ; position restraints for System of [ position_restraints ] ; i funct fcxfcyfcz 51400400400 241400400400 411400400400 481400400400 591400400400 701400400400 861400400400 1071400400400 1261400400400 1401400400400 1561400400400 1711400400400 1901400400400 2001400400400 2191400400400 2291400400400 2451400400400 2641400400400 2741400400400 thank you very much. Albert -- 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
On 8/18/13 1:23 AM, Musharaf Ali 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. I would suggest you spend a while with some tutorial material and the manual to understand the inner mechanics of a normal workflow, then move on to custom residues. Proper implementation is not easy and getting pdb2gmx to deal with a cyclic molecule is not trivial. You will need to define suitable entries in the .rtp file and specbond.dat. Consult the list archive for tips - discussions on cyclic peptides and polymers will have relevant information. -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 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- 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] itp problem
On 8/18/13 2:57 AM, Albert wrote: Hello: I am trying to restrain part of my protein. First I generate a index file by make_ndx. Then I use genrest for this purpose like: genres -f npt.gro -o helix -n -fc 400 after that I change the following in the topol.top file, like: ; Include Position restraint file #ifdef POSRES #include helix.itp #endif when I run grompp, it claimed following warnings: WARNING 1 [file helix.itp, line 1]: Too few parameters on line (source file /home/albert/install/source/gromacs-4.6.3/src/kernel/toppush.c, line 1756) here is my helix.itp: ; position restraints for System of [ position_restraints ] ; i funct fcxfcyfcz 51400400400 241400400400 411400400400 481400400400 591400400400 701400400400 861400400400 1071400400400 1261400400400 1401400400400 1561400400400 1711400400400 1901400400400 2001400400400 2191400400400 2291400400400 2451400400400 2641400400400 2741400400400 Does replacing helix.itp with the original posre.itp from pdb2gmx fix the problem? I see no reason why this file would cause problems, especially if it was generated by genrestr, so it is important to test whether the original topology works correctly to verify the structure and validity of your #include statements. -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 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- 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 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
[gmx-users] Convert CNS .top into a GROMACS .itp for a small ligand?
Hi, I have a small ligand that apparently PRODRG gets wrong -it completely alters the structure, borks angles etc. making it not what we want. So I used xplo2d to obtain a suitable set of files that I used for docking (with HADDOCK). Now, it seems to me that xplo2d does not output a Gromos ff -compatible .itp file as PRODRG does. However it produces a CNS .top file, which seems to contain most of the same information ( charges, dihedrals, masses etc.) Is there a way to convert between the two? Thanks, Massimo -- 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] Convert CNS .top into a GROMACS .itp for a small ligand?
On 8/18/13 3:37 PM, massimo sandal wrote: Hi, I have a small ligand that apparently PRODRG gets wrong -it completely alters the structure, borks angles etc. making it not what we want. So I used xplo2d to obtain a suitable set of files that I used for docking (with HADDOCK). Interesting. The hallmark of the PRODRG development process was that bonded geometries were very well maintained. I have never seen such a problem; the issues were always with the charges. Now, it seems to me that xplo2d does not output a Gromos ff -compatible .itp file as PRODRG does. However it produces a CNS .top file, which seems to contain most of the same information ( charges, dihedrals, masses etc.) Is there a way to convert between the two? Yes, but it will involve using multiple files. The CNS topology should be reasonably straightforward to parse with, e.g. Perl, but you will have to cross-reference bonded parameters from ffbonded.itp by atom type and somehow assign charge groups (although that can be done manually after the fact, if needed). -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 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- 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
[gmx-users] want to apply electric field in membrane system
Hi All, I am facing a strange problem when I was trying to apply electric field across a membrane, DMPC, water and ion system. To apply electric field across the membrane (in +ve z direction), I had used NPzAT ensemble, where the Pz is the constant pressure along the z direction and A is the constant area in xy plane. The following essential keywords were used to construct such kind of system. Pcoupltype = anisotropic tau_p= 1.0 1.0 compressibility = 0.0 0.0 3e-4 0.0 0.0 0.0 ref_p= 0.0 0.0 1.0 0.0 0.0 0.0 ;Electric fileld E-z = 1 2.0 0 Here, I had chosen anisotropic coupling and two tau_ps are for two groups(DMPC and water_ion). The compressibility for x, y and off diagonal elements were chosen as 0 and the compressibility in z direction was chosen as 3e-4. Logically, such compressibility factors ensures that area in xy plane will not change. However, I am not getting the expected results. The strange thing is that the bilayer and water mixed up, the lengths of box abruptly are changed in three directions, and the water molecules are arranged in a linear fashion (I think it is due to the effect of electric field). May be the electric field is high enough and as a result the electroporation occurs very rapidly. Moreover, the are area in xy plane is not fixed, they are changing abruptly. I don't understand why does it happen. This is because the compressibilities are zero along x and y directions. Another strange thing is that there are too many LINCS warning. How do I resolve this issue. Please help me out in this regard. Thanks in advance shen -- 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
[gmx-users] Insertion Events
Hello friends Can anyone suggest how to perform the Correlation between insertion of water molecules into α-helical hydrogen bonds and the formation of turn and π-helical conformations. http://gromacs.5086.x6.nabble.com/file/n5010574/img.png If it is any commands to perform the above analysis please let me know. -- View this message in context: http://gromacs.5086.x6.nabble.com/Insertion-Events-tp5010574.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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
