Dear Justin, Thank you for your full explanation. That made it all clear now.
Kind regards, Ali > On 13 Nov 2018, at 00:57, Justin Lemkul <jalem...@vt.edu> wrote: > > > > On 11/8/18 1:37 PM, Ali Khodayari wrote: >> Dear Justin, >> >> Thank you for your response. Yet, I have not been able to solve the problem. >> >> The structure looks fine but gromacs is complaining about a dangling atom at >> one of the terminal ends, if I choose no terminal to be added. While, > > You can't "see" a dangling bond by visualizing the structure. That term > refers exclusively to an incomplete terminus in terms of the *topology* that > is being generated for the system. Maybe atoms are missing or an > inappropriate terminal patch is being applied; either would generate that > error. But again I emphasize the fact that a chain of glucose has first and > last residues that are structurally and topologically different from > internal, linked monomers. It's basic chemistry. > > <snip> > >> ATOM 27 O3 GLC0 2 3.909 5.661 5.002 1.00 0.04 >> O >> ATOM 28 HO4 GLC0 2 4.850 3.729 10.263 1.00 0.00 >> H >> ATOM 29 O1 GLC0 1 3.396 2.685 4.467 1.00 0.04 >> O > > Here's your problem - your residue numbers alternate back and forth between 1 > and 2. pdb2gmx ignores these and uses its own numbering, incrementing the > internal counter whenever the residue number changes. So to pdb2gmx, your > input file is full of incomplete residues. > >> ATOM 30 O5 GLC0 2 4.225 2.770 8.173 1.00 0.04 >> O >> ATOM 31 O6 GLC0 2 3.558 0.309 5.328 1.00 0.04 >> O >> ATOM 32 H1 GLC0 2 2.572 4.115 8.609 1.00 0.00 >> H >> ATOM 33 H2 GLC0 2 5.244 5.151 7.307 1.00 0.00 >> H >> ATOM 34 H3 GLC0 2 2.361 4.651 6.153 1.00 0.00 >> H >> ATOM 35 H4 GLC0 2 5.141 3.258 5.636 1.00 0.00 >> H >> ATOM 36 H5 GLC0 2 2.480 2.262 6.979 1.00 0.00 >> H >> ATOM 37 H61 GLC0 2 3.879 0.196 7.468 1.00 0.00 >> H >> ATOM 38 H62 GLC0 2 5.286 0.920 6.494 1.00 0.00 >> H >> ATOM 39 HO2 GLC0 2 2.496 6.480 7.836 1.00 0.00 >> H >> ATOM 40 HO3 GLC0 2 5.015 5.674 4.919 1.00 0.00 >> H >> ATOM 41 HO6 GLC0 2 2.453 0.270 5.418 1.00 0.00 >> H >> ATOM 42 O3 GLC0 1 3.852 1.653 -0.348 1.00 0.00 >> O > > As above, now you're again going back and forth between 1 and 2, so pdb2gmx > sees a new residue, which is not correct. > > -Justin > > -- > ================================================== > > Justin A. Lemkul, Ph.D. > Assistant Professor > Virginia Tech Department of Biochemistry > > 303 Engel Hall > 340 West Campus Dr. > Blacksburg, VA 24061 > > jalem...@vt.edu | (540) 231-3129 > http://www.thelemkullab.com > > ================================================== > > -- > 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.
