[gmx-users] Error when try obtain protein energies instead of system energies

[Rodrigo Faccioli]

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
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