hello everybody i am trying to setup the position restrained dynamics but failed to proceed,-
in terminal window it shows the massage- calling /usr/bin/cpp... processing topology... Generated 1284 of the 1485 non-bonded parameter combinations Excluding 3 bonded neighbours for Protein 1 turning all bonds into constraints... Excluding 3 bonded neighbours for UNK 1 turning all bonds into constraints... Excluding 2 bonded neighbours for SOL 44524 turning all bonds into constraints... Excluding 1 bonded neighbours for Cl 16 turning all bonds into constraints... processing coordinates... double-checking input for internal consistency... Velocities were taken from a Maxwell distribution at 300 K Reading position restraint coords from god_b4em.pdb renumbering atomtypes... converting bonded parameters... # ANGLES: 6075 # PDIHS: 2098 # IDIHS: 2246 # LJ14: 7545 # POSRES: 3088 # CONSTR: 4142 # SETTLE: 44524 Walking down the molecule graph to make shake-blocks initialising group options... processing index file... Analysing residue names: Opening library file /usr/share/gromacs/top/aminoacids.dat There are: 44541 OTHER residues There are: 396 PROTEIN residues There are: 0 DNA residues Analysing Protein... Analysing Other... WARNING 1 [file aminoacids.dat, line 1]: T-Coupling group Protein has fewer than 10% of the atoms (4007 out of 137634) Maybe you want to try Protein and Non-Protein instead? Making dummy/rest group for Acceleration containing 137634 elements Making dummy/rest group for Freeze containing 137634 elements Making dummy/rest group for Energy Mon. containing 55 elements Making dummy/rest group for VCM containing 137634 elements Number of degrees of freedom in T-Coupling group Protein is 7921.91 Number of degrees of freedom in T-Coupling group Non-Protein is 267263.09 Making dummy/rest group for User1 containing 137634 elements Making dummy/rest group for User2 containing 137634 elements Making dummy/rest group for XTC containing 137634 elements Making dummy/rest group for Or. Res. Fit containing 137634 elements Making dummy/rest group for QMMM containing 137634 elements T-Coupling has 2 element(s): Protein Non-Protein Energy Mon. has 3 element(s): Protein SOL rest 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): rest 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 pr.tpr to ./#pr.tpr.2# There was 1 warning gcq#194: "You Crashed Into the Swamps" (Silicon Graphics) r...@bioinfo-desktop:/usr/local/gromacs/god2# nohup mdrun -deffnm pr & [1] 6846 nohup: ignoring input and appending output to `nohup.out' any body can recognize the error,i am attaching the pr.mdp file. Thank you have nice day. AKALABYA BISSOYI NIT ROURKELA,INDIA
pr.mdp
Description: Binary data
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