Hi,
I used this method recently and I was experiencing the same errors. As Mark suggested, makes sure your protein survives an energy minimisation. My error was a result of poor preparation of the .pdb file before running pdb2gmx. My .itp file contained a long bond between the C and N termini of a dimer. IF you have any doubts, try running InflateGRO2 using a very small part of your protein (1 chain) and see if it works. Anthony On 24/08/2015 08:59, "Mark Abraham" <mark.j.abra...@gmail.com> wrote: >Hi, > >Something isn't stable. Check that your membrane protein survives a vacuum >EM (at least). And check your parameter settings for inflategro. > >Mark > >On Mon, Aug 24, 2015 at 9:53 AM Yasser Almeida Hernández < >yasser.almeida.hernan...@chemie.uni-hamburg.de> wrote: > >> Hi all, >> >> I want to insert a membrane protein into a model bilayer and I've tried >> several methods. The more straightforward seems to be Memembed, which >> gives an orientation to the membrane. On the other hand this method only >> outputs the "membrane" as dummy balls. How to translate this orientation >> to a model bilayer (DOPC, POPC)? >> >> On the other hand I've tried InflateGRO2 for this purpose and I got this >> error (following the tutorial in >> https://code.google.com/p/inflategro2/wiki/TutorialTolC ): >> >> Back Off! I just backed up ../1-topology/4hzuS_popc.top to >> ../1-topology/#4hzuS_popc.top.3# >> Will use a deflating factor of 0.925539817285086 to shrink the lipids >> back in 20 steps >> Deflating >> grompp -f deflate.mdp -c inflated.gro -p ../1-topology/4hzuS_popc.top -n >> inflated.ndx -o tmp.tpr -maxwarn 1 >> mdrun -s tmp.tpr -v -deffnm tmp_out -c shrink.00.gro >> --------------------------------- >> ERROR: Cannot open GRO file "shrink.00.gro": No such file or directory >> >> >> The end of the log.out file is this: >> >> Fatal error: >> Too many LINCS warnings (1184) >> If you know what you are doing you can adjust the lincs warning >> threshold in your mdp file or set the environment variable >> GMX_MAXCONSTRWARN to -1, but normally it is better to fix the problem >> >> Any thoughts? >> >> Thanks in advance >> >> -- >> Yasser Almeida Hernández >> PhD student >> Institute of Biochemistry and Molecular Biology >> Department of Chemistry >> University of Hamburg >> Martin-Luther-King-Platz 6 >> 20146 Hamburg >> Germany >> +49 40 42838 2845 >> yasser.almeida.hernan...@chemie.uni-hamburg.de >> office: Grindelallee 117, room 250c >> >> -- >> 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. -- 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.
