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

Thu Aug 29 10:24:00 CEST 2013

Hi Sri,

I guess that this simulation was run through the WeNMR GMX portal? It's not
really a Gromacs question. Problems with that portal should be directed to
the adminstrator, who will send it to me anyway, so I'll respond here :)

The error means 1. that I should put time in writing more clear error
messages and 2. that mdrun finished with a non-zero exit value in step 7:
NpT equilibration. The actual error can be found in the log file for that
step in the archive 07-NPT-*.log If you can send me that log file
(off-list), then I can have a closer look.

Best,

Tsjerk

On Thu, Aug 29, 2013 at 8:15 AM, sri2201 <penumutchu.srinivas at gmail.com>wrote:

> 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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-- 
Tsjerk A. Wassenaar, Ph.D.