Hi I used the command. grompp -f fullmd.mdp -c minimized_water.gro -p xxx.top -o fullmd.tpr It showed the following WARNING. WARNING 1 [file aminoacids.dat, line 1]
My system did not include any protein. So, could I skip/neglect the WARNING?? Thank you Lin The following is the message after send the above command. creating statusfile for 1 node... Back Off! I just backed up mdout.mdp to ./#mdout.mdp.2# checking input for internal consistency... calling /usr/libexec/gcc/darwin/ppc/3.3/cpp... processing topology... Generated 141 of the 1176 non-bonded parameter combinations Excluding 3 bonded neighbours for azoct 1 Excluding 2 bonded neighbours for SOL 1209 NOTE: System has non-zero total charge: 1.000000e+00 processing coordinates... double-checking input for internal consistency... Velocities were taken from a Maxwell distribution at 300 K renumbering atomtypes... converting bonded parameters... # G96BONDS: 34 # G96ANGLES: 50 # PDIHS: 64 # IDIHS: 12 # LJ14: 11 # SETTLE: 1209 initialising group options... processing index file... Analysing residue names: Opening library file /usr/local/gromacs/share/gromacs/top/aminoacids.dat There are: 1210 OTHER residues There are: 0 PROTEIN residues There are: 0 DNA residues Analysing Other... WARNING 1 [file aminoacids.dat, line 1]: T-Coupling group azoct has fewer than 10% of the atoms (33 out of 3660) Maybe you want to try Protein and Non-Protein instead? Making dummy/rest group for Acceleration containing 3660 elements Making dummy/rest group for Freeze containing 3660 elements Making dummy/rest group for VCM containing 3660 elements Number of degrees of freedom in T-Coupling group azoct is 98.96 Number of degrees of freedom in T-Coupling group SOL is 7251.04 Making dummy/rest group for User1 containing 3660 elements Making dummy/rest group for User2 containing 3660 elements Making dummy/rest group for Or. Res. Fit containing 3660 elements Making dummy/rest group for QMMM containing 3660 elements T-Coupling has 2 element(s): azoct SOL Energy Mon. has 2 element(s): azoct SOL Acceleration has 1 element(s): rest Freeze has 1 element(s): rest User1 has 1 element(s): rest User2 has 1 element(s): rest VCM has 1 element(s): rest XTC has 1 element(s): azoct Or. Res. Fit has 1 element(s): rest QMMM has 1 element(s): rest Checking consistency between energy and charge groups... writing run input file... Back Off! I just backed up fullmd.tpr to ./#fullmd.tpr.1# There was 1 warning gcq#293: "There's Still Time to Change the Rope You're On" (Led Zeppelin) _______________________________________________ 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
