Re: [gmx-users] How to avoid generating wrong dihedrals?
Hi Chaofu Wu, Indeed it seems improper to have a dihedral with C-N-H-H. So it's an improper dihedral! :p The problem might arise from the addition of hydrogens. Could you give more information? Which force field did you use? what residue was causing the problem? Can you reproduce the problem starting only with that residue (and then paste it, so that one of us might reproduce it)? Cheers, Tsjerk 2009/7/1 wuxiao xiaowu...@hotmail.com: Dear gmx users, I try to generate gro and top files using pdb2gmx, and this procedure finishs without any error. However, when I run grompp from these files, many errors are encountered such as: .. ERROR 124 [file g04.top, line 20027] No default Ryckaert-Bell. types .. I gusess it is dihedrals that cause these errors. So I look for the line 20027 in the file g04.top. only to find that these dihedrals are C-N-H-H, obviously wrong. How to avoid these errors? Could you give me some help to cope with them? Thank you for attention. Sincerely, Chaofu Wu 把MSN装进手机，更多聊天乐趣等你挖掘！ 立刻下载！ ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] How to avoid generating wrong dihedrals?(Tsjerk)
Dear Tsjerk and other gmx users and developers, I use OPLS-AA force field to model a dendrimer PAMAM. And the addition of hydrogens is found correct. The rtp files were written for the core, middle and end repeating units, respectively. The both repeating units cause the problem. When I delete all those wrong dihedrals in the top file, the grompp and mdrun can run successfully. I check the top file. It seems that other dihedrals are all correct. What to happen to this? Could you give me further information? Any reply would be thanked very much. Sincerely, Chaofu Wu Hi Chaofu Wu, Indeed it seems improper to have a dihedral with C-N-H-H. So it's an improper dihedral! :p The problem might arise from the addition of hydrogens. Could you give more information? Which force field did you use? what residue was causing the problem? Can you reproduce the problem starting only with that residue (and then paste it, so that one of us might reproduce it)? Cheers, Tsjerk _ 打工，挣钱，买房子，快来MClub一起”金屋藏娇”！ http://club.msn.cn/?from=10___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] How to avoid generating wrong dihedrals?(Tsjerk)
wuxiao wrote: Dear Tsjerk and other gmx users and developers, I use OPLS-AA force field to model a dendrimer PAMAM. And the addition of hydrogens is found correct. The rtp files were written for the core, middle and end repeating units, respectively. The both repeating units cause the problem. When I delete all those wrong dihedrals in the top file, the grompp and mdrun can run successfully. I check the top file. It seems that other dihedrals are all correct. What to happen to this? Could you give me further information? Any reply would be thanked very much. I think it likely you have a malformed [ dihedrals ] section in your .rtp file. pdb2gmx will generate dihedrals for each rotatable bond (see manual section 5.6.1), so the only way you can get such a dihedral is to have defined all three of those bonds, or specifically defined that dihedral. Perhaps these bonds are being created erroneously by your .hdb? You will have to look in detail at what you are doing with these. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] How to avoid generating wrong dihedrals?
Dear gmx users, I try to generate gro and top files using pdb2gmx, and this procedure finishs without any error. However, when I run grompp from these files, many errors are encountered such as: .. ERROR 124 [file g04.top, line 20027] No default Ryckaert-Bell. types .. I gusess it is dihedrals that cause these errors. So I look for the line 20027 in the file g04.top. only to find that these dihedrals are C-N-H-H, obviously wrong. How to avoid these errors? Could you give me some help to cope with them? Thank you for attention. Sincerely, Chaofu Wu _ 打工，挣钱，买房子，快来MClub一起”金屋藏娇”！ http://club.msn.cn/?from=10___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
