[gmx-users] double bond
Hi gromacs users, In my nafion sidechain, I have -CF2-SO3H. In this molecule, S atom has 2 double bonds with 2 O, 1 single bond with another O, and i single bond with C (total 6 bonds). When I do energy minimization in vacuum, I got two F atoms nonbonded to my C atom. I think, gromacs generate triple bonds between C and S and 3 single bonds between S and 3 O atoms. I added these commands in specbond.dat to resolve the issue NAF S 6 NAF O4 2 0.3 NAF NAF NAF S 6 NAF O5 2 0.3 NAF NAF But, it didn't solve my problem. Any suggestion for solving this problem? Regards, Ehsan -- 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] double bond
On 10/3/13 3:08 PM, Ehsan Sadeghi wrote: Hi gromacs users, In my nafion sidechain, I have -CF2-SO3H. In this molecule, S atom has 2 double bonds with 2 O, 1 single bond with another O, and i single bond with C (total 6 bonds). When I do energy minimization in vacuum, I got two F atoms nonbonded to my C atom. I think, gromacs generate triple bonds between C and S and 3 single bonds between S and 3 O atoms. I added these commands in specbond.dat to resolve the issue NAF S 6 NAF O4 2 0.3 NAF NAF NAF S 6 NAF O5 2 0.3 NAF NAF But, it didn't solve my problem. Any suggestion for solving this problem? There is no distinction between a single, double, or triple bond in an MM force field, and Gromacs certainly doesn't change anything about the bonds. If your desired geometry isn't being preserved, choose or derive better bonded parameters. Also note that bonds will not break; visualization software often guesses bonds incorrectly. What you see is not definitive. What is written in the topology is. -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] double bond
Thanks Justin. I will try different bond parameters. I usually use PyMol or Chimera for visualization. Do you have any recommendation for a visualization software? Cheers, Ehsan - Original Message - From: Justin Lemkul jalem...@vt.edu To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Thursday, October 3, 2013 1:09:05 PM Subject: Re: [gmx-users] double bond On 10/3/13 3:08 PM, Ehsan Sadeghi wrote: Hi gromacs users, In my nafion sidechain, I have -CF2-SO3H. In this molecule, S atom has 2 double bonds with 2 O, 1 single bond with another O, and i single bond with C (total 6 bonds). When I do energy minimization in vacuum, I got two F atoms nonbonded to my C atom. I think, gromacs generate triple bonds between C and S and 3 single bonds between S and 3 O atoms. I added these commands in specbond.dat to resolve the issue NAF S 6 NAF O4 2 0.3 NAF NAF NAF S 6 NAF O5 2 0.3 NAF NAF But, it didn't solve my problem. Any suggestion for solving this problem? There is no distinction between a single, double, or triple bond in an MM force field, and Gromacs certainly doesn't change anything about the bonds. If your desired geometry isn't being preserved, choose or derive better bonded parameters. Also note that bonds will not break; visualization software often guesses bonds incorrectly. What you see is not definitive. What is written in the topology is. -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 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] double bond
On 10/3/13 4:15 PM, Ehsan Sadeghi wrote: Thanks Justin. I will try different bond parameters. I usually use PyMol or Chimera for visualization. Do you have any recommendation for a visualization software? For quick visualization, VMD (but it often gets bonds wrong if they are not in line with its assumptions) and for rendering images and movies, PyMOL. It's all a matter of personal preference. None of them is perfect. -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
