[gmx-users] ERROR : GROMACS finsihed with error 74

[sri2201]

Dear Gromacs , 

I running the md simulation for protein complex (44 kd ) with amber99sb-ildn
force filed . iam getting error as follows , looks like it is syntax error .

Input file: gmx-495644.pdb Base name: gmx-495644 Source directory:
/scratch/home/enmr028/home_cream_840250368/CREAM840250368 GROMACS mdrun will
run for a maximum of hours. (voms proxy lifetime 0 sec.) Starting MD
protocol for
/scratch/home/enmr028/home_cream_840250368/CREAM840250368/gmx-495644.pdb
Using amber force field amber99sb-ildn with tip3p water model Using PME for
treatment of long range coulomb interactions Not using virtual sites
Simulations will be performed in a rhombic dodecahedron unit cell 7500000
#---= THIS IS WHERE WE START =-- #---STEP 1A: GENERATE STRUCTURE AND
TOPOLOGY FOR INPUT PDB FILE Wed Aug 28 17:54:19 BST 2013:
/mt/experiment-software//enmr/BCBR/gromacs/4.5.3-rtc/bin/pdb2gmx -v -f
/scratch/home/enmr028/home_cream_840250368/CREAM840250368/gmx-495644.pdb -o
gmx-495644.gro -p gmx-495644.top -ignh -ff amber99sb-ildn -water tip3p -i
gmx-495644-posre.itp -posrefc 999 Removing duplicate moleculetype definition
in gmx-495644_Protein_chain_D.itp #---STEP 1B: ADD LIGANDS SPECIFIED ON
COMMAND LINE #---STEP 2: SET PERIODIC BOUNDARY CONDITIONS Wed Aug 28
17:54:21 BST 2013:
/mt/experiment-software//enmr/BCBR/gromacs/4.5.3-rtc/bin/editconf -f
gmx-495644.gro -o gmx-495644-pbc.gro -bt dodecahedron -d 1.125 -c #---STEP
3: RUN EM IN VACUUM Wed Aug 28 17:54:21 BST 2013:
/mt/experiment-software//enmr/BCBR/gromacs/4.5.3-rtc/bin/grompp -f
em-vac.mdp -po em-vac-out.mdp -c gmx-495644-pbc.gro -p gmx-495644.top -o
gmx-495644-EMv.tpr -maxwarn 1 Wed Aug 28 17:54:21 BST 2013:
/mt/experiment-software//enmr/BCBR/gromacs/4.5.3-rtc/bin/mdrun -nice 0
-deffnm gmx-495644-EMv -c gmx-495644-EMv.gro -cpi gmx-495644-EMv.cpt -nt 1
-maxh 12000 Wed Aug 28 17:54:29 BST 2013: FINISHED MDRUN EMVACUUM #---STEP
4: SOLVATION AND ADDING IONS Wed Aug 28 17:54:29 BST 2013:
/mt/experiment-software//enmr/BCBR/gromacs/4.5.3-rtc/bin/genbox -cp
gmx-495644-EMv.gro -cs -o gmx-495644-sol-b4ions.gro Solvent added: 25839
molecules Wed Aug 28 17:54:30 BST 2013:
/mt/experiment-software//enmr/BCBR/gromacs/4.5.3-rtc/bin/grompp -v -f
empty.mdp -c gmx-495644-sol-b4ions.gro -p gmx-495644-sol-b4ions.top -o
gmx-495644-sol-b4ions.tpr -po defaults.mdp -maxwarn 1 Net charge of system:
6 Replacing 142 solvent molecules with 68 NA (1) and 74 CL (-1) ions. Wed
Aug 28 17:54:33 BST 2013:
/mt/experiment-software//enmr/BCBR/gromacs/4.5.3-rtc/bin/genion -s
gmx-495644-sol-b4ions.tpr -o gmx-495644-sol.gro -g genion.log -n sol.ndx -pq
1 -nn 74 -np 68 -pname NA -nname CL -nq -1 -rmin 0.5 -random #---STEP 5:
ENERGY MINIMIZATION IN SOLVENT (NVT) Wed Aug 28 17:54:38 BST 2013:
/mt/experiment-software//enmr/BCBR/gromacs/4.5.3-rtc/bin/grompp -f
em-sol.mdp -po em-sol-out.mdp -c gmx-495644-sol.gro -p gmx-495644-sol.top -o
gmx-495644-EMs.tpr -maxwarn 1 Wed Aug 28 17:54:39 BST 2013:
/mt/experiment-software//enmr/BCBR/gromacs/4.5.3-rtc/bin/mdrun -nice 0
-deffnm gmx-495644-EMs -c gmx-495644-EMs.gro -cpi gmx-495644-EMs.cpt -nt 1
-maxh 12000 Wed Aug 28 17:56:49 BST 2013: FINISHED MDRUN EMSOLVENT #---STEP
6: POSITION RESTRAINT MD, NVT -- CYCLE THROUGH PRFC AND TEMP/TAU_T Solute
Solvent Equilibration (NVT/PR): Temperatures: 300.0 Coupling times: 0.1
Position restraint Fcs: 200 200 200 NVT Equilibration at 300.0 Kelvin
(tau_t=0.1) with Position restraint force 200 Wed Aug 28 17:56:54 BST 2013:
/mt/experiment-software//enmr/BCBR/gromacs/4.5.3-rtc/bin/grompp -f
pr-200-nvt-300.0-0.1.mdp -po pr-200-nvt-300.0-0.1-out.mdp -c
gmx-495644-EMs.gro -p gmx-495644-sol.top -n gmx-495644-sol.ndx -o
gmx-495644-PR-200-NVT-300.0-0.1.tpr -maxwarn 1 -r gmx-495644-EMs.gro Wed Aug
28 17:56:55 BST 2013:
/mt/experiment-software//enmr/BCBR/gromacs/4.5.3-rtc/bin/mdrun -nice 0
-deffnm gmx-495644-PR-200-NVT-300.0-0.1 -c
gmx-495644-PR-200-NVT-300.0-0.1.gro -cpi gmx-495644-PR-200-NVT-300.0-0.1.cpt
-nt 1 -maxh 12000 Thu Aug 29 03:04:27 BST 2013: FINISHED MDRUN NVT-PR 200
NVT Equilibration at 300.0 Kelvin (tau_t=0.1) with Position restraint force
200 Output found (gmx-495644-PR-200-NVT-300.0-0.1.gro). Skipping step NVT-PR
#---STEP 7: UNRESTRAINED MD 20 ps NPT -- CYCLE THROUGH PRESSURE/TAU_P
Equilibration (NpT): Pressures: 1.01325 Coupling times: 0.5 NpT
Equilibration at 1.01325 bar (tau_p=0.5) Thu Aug 29 03:05:00 BST 2013:
/mt/experiment-software//enmr/BCBR/gromacs/4.5.3-rtc/bin/grompp -f
npt-1.01325-0.5.mdp -po npt-1.01325-0.5-out.mdp -c
gmx-495644-PR-200-NVT-300.0-0.1.gro -p gmx-495644-sol.top -n
gmx-495644-sol.ndx -o gmx-495644-NPT-1.01325-0.5.tpr -maxwarn 1 -r
gmx-495644-EMs.gro Thu Aug 29 03:05:01 BST 2013:
/mt/experiment-software//enmr/BCBR/gromacs/4.5.3-rtc/bin/mdrun -nice 0
-deffnm gmx-495644-NPT-1.01325-0.5 -c gmx-495644-NPT-1.01325-0.5.gro -cpi
gmx-495644-NPT-1.01325-0.5.cpt -nt 1 -maxh 12000 Thu Aug 29 06:04:39 2013 

MDS ERROR : GROMACS finsihed with error 74,

Please suggest me to aviod this bug or my input errors .

Thanking you in advance .



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