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