Dear gromacs users, I’m planing to perform several CG simulations of different biological membranes in the presence of an specific protein. In order to create the membranes, i’m currently using the insane script to make different kind of mixture (POPC alone, POPC-MGDG 5:5, POPC-SQDG 5:5, and POPC-DGDG 5.5) as following: ./insane.py -f minimization-vaccum.gro -o system.gro -pbc square -dm 5 -box 10,10,10 -l DGDG:5 -l POPC:5 -sol W -orient The problem arise when i tried to add ions in order to create a net charge in the last mixture membrane (POPC-DGDG), using the following command line: grompp -f ions.mdp -c system.gro -p system.top -o ions.tpr
Getting the following warning message: Warning: atom name 177 in system.top and system.gro does not match (GA1 - GB2) Warning: atom name 178 in system.top and system.gro does not match (GA2 - GB3) Warning: atom name 179 in system.top and system.gro does not match (GA3 - GB1) Warning: atom name 180 in system.top and system.gro does not match (GB1 - GA1) Warning: atom name 181 in system.top and system.gro does not match (GB2 - GA2) Warning: atom name 182 in system.top and system.gro does not match (GB3 - GA3) (more than 20 non-matching atom names) Looking into the .itp file (martini_v2.0_glycolipids.itp) i found that the atoms GA1, GA2, GA3, GB1, GB2 and GB3 are described in a different order between the *itp file and the *gro file (where first is described the GB2 atom, followed by GB3, GB1, GA1,GA2 and finally GA3) created by insane script. My question is, it is ok if i just change the order in the *itp file, to make it identical as the one found in the *gro file? If not, what should i do in order to avoid any kind of issue during the simulation?. Thanks in advance Best regards, Carlos -- Carlos Navarro Retamal Bioinformatics Engineering Ph. D (c) Applied Sciences. Center of Bioinformatics and Molecular Simulations. CBSM University of Talca Av. Lircay S/N, Talca, Chile T: (+56) 712201 798 E: carlos.navarr...@gmail.com or cnava...@utalca.cl -- 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.
