Re: [gmx-users] error in umbrella sampling tutorial
http://lmgtfy.com/?q=There+is+a+dangling+bond+at+at+least+one+of+the+terminal+ends.+Fix+your+coordinate+file%2C+add+a+new+terminal+database+entry+(.tdb)%2C+or+select+the+proper+existing+terminal+entry . On Thu, Apr 23, 2015 at 8:47 AM, Ayesha Fatima ayeshafatima...@gmail.com wrote: Dear Justin, I am learning to use the steered dynamics method implemented in gromacs. somehow your website is not accessible today so i cannot download the modified files of the fibrils for simulation. so i started withe the original file 2BEG.pdb and if i dont select the N and C termini modifications i get the error ... There is a dangling bond at at least one of the terminal ends. Fix your coordinate file, add a new terminal database entry (.tdb), or select the proper existing terminal entry. . Could you guide me through the issue? Thank you Regards Ayesha Fatima PhD candidate, UM, Malaysia -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] error in umbrella sampling tutorial
On 4/23/15 8:47 AM, Ayesha Fatima wrote: Dear Justin, I am learning to use the steered dynamics method implemented in gromacs. somehow your website is not accessible today so i cannot Server has been accessible all day; no idea why it wouldn't be working. download the modified files of the fibrils for simulation. so i started withe the original file 2BEG.pdb and if i dont select the N and C termini modifications i get the error ... There is a dangling bond at at least one of the terminal ends. Fix your coordinate file, add a new terminal database entry (.tdb), or select the proper existing terminal entry. . Could you guide me through the issue? You can't sensibly choose none for terminal patching if there are no capping groups. My coordinates have an acetyl cap on the N-terminus of each peptide, which is why this works. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
