Hi, I tried to obtain the energies of protein instead of system energies. However, when I execute the last command, I received the message below:
Reading file /home/faccioli/Execute/EESC_AE/1A11/prot_alone.tpr, VERSION 4.5.4 (single precision) Starting 2 threads Making 1D domain decomposition 2 x 1 x 1 starting md rerun 'PROTEIN 10.500000 390 in water', reading coordinates from input trajectory '/home/faccioli/Execute/EESC_AE/1A11/prot_alone.trr' trn version: GMX_trn_file (single precision) Reading frame 0 time 0.000 ------------------------------------------------------- Program mdrun, VERSION 4.5.4 Source code file: /home/faccioli/gromacs-4.5.4/src/kernel/md.c, line: 1623 Fatal error: Number of atoms in trajectory (390) does not match the run input file (20524) For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors ------------------------------------------------------- All steps which I ran they are below. The bold part shows the step where you can found the error. #pdb2gmx /usr/local/bin/./pdb2gmx -f /home/faccioli/Execute/EESC_AE/1A11/PROT_IND_FINAL_0.pdb -o /home/faccioli/Execute/EESC_AE/1A11/prot_sys.gro -ff charmm27 -water spc -p /home/faccioli/Execute/EESC_AE/1A11/prot_sys.top -ignh > protpred-Gromacs_compute.log #editconf /usr/local/bin/./editconf -f /home/faccioli/Execute/EESC_AE/1A11/prot_sys.gro -o /home/faccioli/Execute/EESC_AE/1A11/prot_sys_newbox.gro -bt cubic -c -d 1.2 > protpred-Gromacs_compute.log #genbox /usr/local/bin/./genbox -cp /home/faccioli/Execute/EESC_AE/1A11/prot_sys_newbox.gro -p /home/faccioli/Execute/EESC_AE/1A11/prot_sys.top -o /home/faccioli/Execute/EESC_AE/1A11/prot_sys_solv.gro -cs spc216 > protpred-Gromacs_compute.log #grompp - prepare to add ions /usr/local/bin/./grompp -f /home/faccioli/Execute/EESC_AE/1A11/ions.mdp -p /home/faccioli/Execute/EESC_AE/1A11/prot_sys.top -o /home/faccioli/Execute/EESC_AE/1A11/prot_sys.tpr -c /home/faccioli/Execute/EESC_AE/1A11/prot_sys_solv.gro > protpred-Gromacs_compute.log #genion echo -e 13 | /usr/local/bin/./genion -s /home/faccioli/Execute/EESC_AE/1A11/prot_sys.tpr -o /home/faccioli/Execute/EESC_AE/1A11/prot_sys_solv_ions.gro -p /home/faccioli/Execute/EESC_AE/1A11/prot_sys.top -pname NA -nname CL -neutral -conc 0.0000001 -random -seed -1 #grompp - prepare to compute the energy /usr/local/bin/./grompp -f /home/faccioli/Execute/EESC_AE/1A11/compute_energy.mdp -p /home/faccioli/Execute/EESC_AE/1A11/prot_sys.top -o /home/faccioli/Execute/EESC_AE/1A11/prot_sys.tpr -c /home/faccioli/Execute/EESC_AE/1A11/prot_sys_solv_ions.gro > protpred-Gromacs_compute.log #mdrun - computes the energies /usr/local/bin/./mdrun -s /home/faccioli/Execute/EESC_AE/1A11/prot_sys.tpr -o /home/faccioli/Execute/EESC_AE/1A11/prot_sys.trr -c /home/faccioli/Execute/EESC_AE/1A11/prot_sys.gro -e /home/faccioli/Execute/EESC_AE/1A11/energy.xvg -g /home/faccioli/Execute/EESC_AE/1A11/prot_sys.log > protpred-Gromacs_compute.log # trjconv - to obatin prot_alone.trr echo 1 | /usr/local/bin/./trjconv -f /home/faccioli/Execute/EESC_AE/1A11/prot_sys.trr -s /home/faccioli/Execute/EESC_AE/1A11/prot_sys.tpr -o /home/faccioli/Execute/EESC_AE/1A11/prot_alone.trr # tpbconv - to obtain prot_alone.tpr echo 1 | /usr/local/bin/./tpbconv -s /home/faccioli/Execute/EESC_AE/1A11/prot_sys.tpr -nsteps 1 -o /home/faccioli/Execute/EESC_AE/1A11/prot_alone.tpr -f /home/faccioli/Execute/EESC_AE/1A11/prot_sys.trr # mdrun - it computes protein energies instead of system energies */usr/local/bin/./mdrun -s /home/faccioli/Execute/EESC_AE/1A11/prot_alone.tpr -e /home/faccioli/Execute/EESC_AE/1A11/prot_alone_energy.xvg -rerun /home/faccioli/Execute/EESC_AE/1A11/prot_alone.trr * I used two pdb files. These pdbs and my mdp files are found in [1]. [1] http://dl.dropbox.com/u/4270818/simulation_files.zip Thanks any helps. -- Rodrigo Antonio Faccioli Ph.D Student in Electrical Engineering University of Sao Paulo - USP Engineering School of Sao Carlos - EESC Department of Electrical Engineering - SEL Intelligent System in Structure Bioinformatics http://laips.sel.eesc.usp.br Phone: 55 (16) 3373-9366 Ext 229 Curriculum Lattes - http://lattes.cnpq.br/1025157978990218 Public Profile - http://br.linkedin.com/pub/rodrigo-faccioli/7/589/a5
-- 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
