Hi, I'm doing the KALP-15 IN DPPC through the Justin's tutorial http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/03_solvate.html I have few questions. Please help me to solve it.
1) After the topol.top file has generated from pdb2gmx is it necessary to add DPPC 128 in the molecule section?. 2) I have used DPPC 128 in the molecule section and during adding ions with the following command shows error. grompp -f ions.mdp -c system_solv.gro -p topol.top -o ions.tpr The above command shows this error. Fatal error: number of coordinates in coordinate file (system_solv.gro, 27162) does not match topology (topol.top, 33451) Please tell me where should i change to solve this problem. 3) If i didnt use DPPC in molecule section of .top file while running equilibration using make_ndx which ask us to enter the protein+lipids i could not find the DPPC option there.. please help me to solve this problems. Thanks in advance. -- View this message in context: http://gromacs.5086.x6.nabble.com/KALP-in-DPPC-tutorial-reg-tp5011799.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
