Hello, I have a problem and although I've read almost everything the internet could offer on how differently people have approached this problem, mine hasn't been solved yet.
Basically, I am trying to mix 2 different proteins in one box and after doing my grompp to neutralise the system, I get the error number of coordinates in coordinate file (solvated.gro, 85059) does not match topology (topol.top, 85079). This is how my topology file looks: ;GROMACS toplogy ; ;Include the force field #include "oplsaa.ff/forcefield.itp" ; Include chain topologies #include "topol_1AKI.itp" #include "topol_2CDS.itp" ;Include water topology #include "spce.itp" ;Include generic ion topology #include "ions.itp" [ system ] Two proteins in water [ molecules ] Protein_1AKI 1 Protein_2CDS 1 SOL 27053 How can I deduce from this data that the number of coordinates in topol.top is 85079. And what exactly should I do to reduce the number of molecules here so that the 2 files have the same number of coordinates. I will really appreciate the help. I am pretty new with MD simulations Kind Regards, Chinnu -- View this message in context: http://gromacs.5086.x6.nabble.com/topology-and-coordinate-file-not-matching-after-grompp-tp5010221.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing list gmx-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
