Hello, I want neutralize negative charge in my structure. I use genion to add 80 Na and 71 Cl. Than I edit top file manually to decrease SOL number by 151 and add two lines for ions. Since I use OPLSAA they should look like this (considering names in gromacs/share/gromacs/top/ions.itp)
NA+ 80 CL- 71 When I run grompp afterwards I receive this message: -------------------------------------------------------- Warning: atom name 105260 in 1klc_final_frc.top and 1klc_final_frc.si.gro does not match (NA - Na) Warning: atom name 105261 in 1klc_final_frc.top and 1klc_final_frc.si.gro does not match (NA - Na) (more than 20 non-matching atom names) WARNING 1 [file 1klc_final_frc.top, line 42]: 151 non-matching atom names atom names from 1klc_final_frc.top will be used atom names from 1klc_final_frc.si.gro will be ignored -------------------------------------------------------- That was expected since gro file identifies the ions as "Na" and "Cl", but this is the first time in my experience when grompp throws out this: ------------------------------------------------------- Program grompp, VERSION 4.0.2 Source code file: gmx_fatal.c, line: 481 Fatal error: Too many warnings (1), grompp terminated. If you are sure all warnings are harmless, use the -maxwarn option. ------------------------------------------------------- Is this a problem or should I simply set -maxwarn to 2? Thanks. I appreciate your time. SDA _______________________________________________ gmx-users mailing list [email protected] http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
