Hi all,
I'm trying to simulate a system of POPC- Protein- Water- Ion following the Justin's tutorial of Kalp15-DPPC. I get the system-solved-ion.gro and run energy minimization. I saw some water molecules in em.gro file, therefore, I erase them and then again save the .gro file as a new one. But when I make a new index file, updated the top file and then go through the NVT simulation, I get this fatal error: Warning: atom name 33908 in topol.top and em.gro does not match (HW2 - HW1) Warning: atom name 33909 in topol.top and em.gro does not match (OW - HW2) Warning: atom name 33910 in topol.top and em.gro does not match (HW1 - OW) (more than 20 non-matching atom names) WARNING 1 [file topol.top, line 57]: 43770 non-matching atom names atom names from topol.top will be used atom names from salem.pdb will be ignored Setting gen_seed to 2957 Velocities were taken from a Maxwell distribution at 310 K ------------------------------------------------------- Program grompp, VERSION 4.5.5 Source code file: /home/abuild/rpmbuild/BUILD/gromacs-4.5.5/src/kernel/readir.c, line: 1406 Fatal error: 38 atoms are not part of any of the T-Coupling groups For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors ------------------------------------------------------- Sincerely, Shima -- gmx-users mailing list [email protected] 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 [email protected]. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
