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 . -- View this message in context: http://gromacs.5086.x6.nabble.com/ERROR-GROMACS-finsihed-with-error-74-tp5010801.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists