Hi,<br><br>I tried to obtain the energies of protein instead of system energies. However, when I execute the last command, I received the message below:<br><br>Reading file /home/faccioli/Execute/EESC_AE/1A11/prot_alone.tpr, VERSION 4.5.4 (single precision)<br>
Starting 2 threads<br>Making 1D domain decomposition 2 x 1 x 1<br>starting md rerun &#39;PROTEIN 10.500000 390 in water&#39;, reading coordinates from input trajectory &#39;/home/faccioli/Execute/EESC_AE/1A11/prot_alone.trr&#39;<br>
<br>trn version: GMX_trn_file (single precision)<br>Reading frame       0 time    0.000   <br>-------------------------------------------------------<br>Program mdrun, VERSION 4.5.4<br>Source code file: /home/faccioli/gromacs-4.5.4/src/kernel/md.c, line: 1623<br>
<br>Fatal error:<br>Number of atoms in trajectory (390) does not match the run input file (20524)<br><br>For more information and tips for troubleshooting, please check the GROMACS<br>website at <a href="http://www.gromacs.org/Documentation/Errors">http://www.gromacs.org/Documentation/Errors</a><br>
-------------------------------------------------------<br><br>All steps which I ran they are below. The bold part shows the step where you can found the error. <br><br>#pdb2gmx<br>/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 &gt; protpred-Gromacs_compute.log<br>
#editconf<br>/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  &gt; protpred-Gromacs_compute.log<br>#genbox<br>/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  &gt; protpred-Gromacs_compute.log<br>
#grompp - prepare to add ions<br>/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  &gt; protpred-Gromacs_compute.log<br>
#genion<br>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<br>
#grompp - prepare to compute the energy<br>/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 &gt; protpred-Gromacs_compute.log<br>
#mdrun - computes the energies<br>/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 &gt; protpred-Gromacs_compute.log<br>
# trjconv - to obatin prot_alone.trr<br>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<br>
# tpbconv - to obtain prot_alone.tpr<br>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<br>
# mdrun - it computes protein energies instead of system energies<br><b>/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<br>
</b><br>I used two pdb files. These pdbs and my mdp files are found in [1]. <br><br>[1] <a href="http://dl.dropbox.com/u/4270818/simulation_files.zip">http://dl.dropbox.com/u/4270818/simulation_files.zip</a><br><br>Thanks any helps.<br>
<br clear="all">--<br>Rodrigo Antonio Faccioli<br>Ph.D Student in Electrical Engineering<br>University of Sao Paulo - USP<br>Engineering School of Sao Carlos - EESC<br>Department of Electrical Engineering - SEL<br>Intelligent System in Structure Bioinformatics<br>
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