[gmx-users] Warning: Short Bond pdb2gmx
Dear Gromacs users I did 50ns MD simulation of a protein-ligand complex. From this trajectory, I extracted region of trajectory having stable rmsd and generated an average structure. I want to run this average structure to get an idea of setting some restraints. but when I do gmx pdb2gmx I get following warning:- Warning: Short Bond (9-10 = 0.042416 nm) Warning: Short Bond (9-11 = 0.0463433 nm) Warning: Short Bond (9-12 = 0.0452425 nm) Warning: Short Bond (13-14 = 0.0407501 nm) Warning: Short Bond (13-15 = 0.0425715 nm) Warning: Short Bond (13-16 = 0.0421154 nm) Warning: Short Bond (65-66 = 0.0418464 nm) Warning: Short Bond (65-67 = 0.0454554 nm) Warning: Short Bond (65-68 = 0.0438005 nm) Warning: Short Bond (103-105 = 0.0498706 nm) Warning: Short Bond (103-106 = 0.0482166 nm) Warning: Short Bond (161-162 = 0.0384303 nm) Warning: Short Bond (161-163 = 0.0395632 nm) Warning: Short Bond (161-164 = 0.0404804 nm) Warning: Short Bond (178-179 = 0.0379231 nm) Warning: Short Bond (178-180 = 0.0350074 nm) Warning: Short Bond (178-181 = 0.0367544 nm) Warning: Short Bond (195-197 = 0.0491068 nm) Warning: Short Bond (240-241 = 0.0410752 nm) Warning: Short Bond (240-242 = 0.0400188 nm) Warning: Short Bond (240-243 = 0.0389276 nm) Warning: Short Bond (244-245 = 0.0395354 nm) Warning: Short Bond (244-246 = 0.0394185 nm) Warning: Short Bond (244-247 = 0.0411173 nm) Warning: Short Bond (254-255 = 0.0496385 nm) Warning: Short Bond (254-256 = 0.0490917 nm) Warning: Short Bond (254-257 = 0.0487225 nm) Warning: Short Bond (320-321 = 0.0389006 nm) Warning: Short Bond (320-322 = 0.0354672 nm) Warning: Short Bond (320-323 = 0.0318275 nm) Warning: Short Bond (332-333 = 0.044048 nm) Warning: Short Bond (332-334 = 0.0431301 nm) Warning: Short Bond (332-335 = 0.0443143 nm) Warning: Short Bond (339-340 = 0.0436942 nm) Warning: Short Bond (339-341 = 0.044572 nm) Warning: Short Bond (339-342 = 0.0438389 nm) Warning: Short Bond (386-387 = 0.0485982 nm) Warning: Short Bond (386-388 = 0.0493432 nm) Warning: Short Bond (400-401 = 0.0365161 nm) Warning: Short Bond (400-402 = 0.043 nm) Warning: Short Bond (400-403 = 0.038517 nm) Warning: Short Bond (552-553 = 0.0489085 nm) Warning: Short Bond (552-554 = 0.0483887 nm) Warning: Short Bond (552-555 = 0.0498913 nm) Warning: Short Bond (556-557 = 0.0345456 nm) Warning: Short Bond (556-558 = 0.0396005 nm) Warning: Short Bond (556-559 = 0.0370519 nm) Warning: Short Bond (575-576 = 0.0458407 nm) Warning: Short Bond (575-577 = 0.0455252 nm) Warning: Short Bond (575-578 = 0.0448519 nm) Warning: Short Bond (664-665 = 0.0423401 nm) Warning: Short Bond (664-666 = 0.0390075 nm) Warning: Short Bond (664-667 = 0.0406177 nm) Warning: Short Bond (671-672 = 0.0369435 nm) Warning: Short Bond (671-673 = 0.0354056 nm) Warning: Short Bond (671-674 = 0.0373171 nm) Warning: Short Bond (725-726 = 0.0389842 nm) Warning: Short Bond (725-727 = 0.0393952 nm) I understand that the average structure is not necessarily anything physically meaningful but how I assume that it can give the equilibrium values to set the restraints. I need your help to figure out this warning, please. Thanks in advance. Sadaf -- 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.
[gmx-users] dssp 3.1.4
Good day, I have recently downloaded the latest dssp version and with the mkdssp executable file as I type chmod +x dssp and run this code : gmx do_dssp -f final.xtc -s md.tpr -n index.ndx -o ss.xpm -sc scount.xvg -tu ns the process starts but no output is created after even 1 day my Gormacs version is 2019.3 and even earlier versions of dssp does not work and give me the same result. Till now I have tested this process on 3 computers having GROMACS 2019.3 on them. Can someone help me with this issue? Many thanks. -- *Iman Katouzian* *Ph.D.** candidate of Food Process Engineering* *Faculty of Food Science and Technology* *University of Agricultural Sciences and Natural Resources, Gorgan, Iran* -- 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] PBC after energy minimization
Hi Mohamed, > Hello everybody, > > In order to solve the PBC at the end I use the command: > > *gmx trjconv -s md_0_1.tpr -f md_0_1.xtc -o md_noPBC.xtc -pbc mol * > > followed by: > > *gmx trjconv -s md_0_1.tpr -f md_noPBC.xtc -o md_noPBC.pdb* > > > I want to solve this problem after the energy minimization but I don't > have > .xtc file to use it as I do at the end. > > How can I solve this problem after the energy minimization ? You're saying that your energy minimization does not produce a trajectory (a .trr or .xtc file)? If that's the case, you just have to instruct GROMACS to periodically write to a trajectory file using options in the .mdp file (namely, nstxout). Take a look at: http://manual.gromacs.org/documentation/2018/user-guide/mdp-options.html Under the section "output control" you will find what you are looking for. - John > > Thanks, > Mohamed > -- > 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. > John Whittaker Ph.D. Candidate Department of Mathematics and Computer Science Freie Universität Berlin +49 0160 936 04221 -- 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.
