Dear Sir,<br><br>when i am doing energy minimization (grompp), i found following error<br><br>
CMD : grompp -f em.mdp -c proteinGR_b4ion.gro -p proteinGR.top -o proteinGR_b4ion.tpr<br><br>WARNING 1 [file em.mdp, line unknown]:<br> Unknown or double left-hand 'coulomtype' in parameter file<br><br><br>checking input for internal consistency...<br>
processing topology...<br>Opening library file /usr/share/gromacs/top/ffgmx.itp<br>Opening library file /usr/share/gromacs/top/ffgmxnb.itp<br>Opening library file /usr/share/gromacs/top/ffgmxbon.itp<br>Opening library file /usr/share/gromacs/top/ff_dum.itp<br>
Generated 1284 of the 1485 non-bonded parameter combinations<br><br>-------------------------------------------------------<br>Program grompp, VERSION 4.0.7<br>Source code file: ../../../../src/kernel/toppush.c, line: 947<br>
<br>Fatal error:<br>Atomtype NR not found<br>-------------------------------------------------------<br><br>The parameter file contains,<br><br>title = GR-substrate
<br>cpp = cpp
<br>define = -DFLEX_SPC
<br>constraints = none
<br>integrator = steep
<br>dt = 0.002 ; ps !
<br>nsteps = 100
<br>nstlist = 10
<br>ns_type = grid
<br>rlist = 1.0
<br>coulomtype = PME ; Use particle-mesh ewald
<br>rcoulomb = 1.0
<br>rvdw = 1.0
<br>fourierspacing = 0.12
<br>fourier_nx = 0
<br>fourier_ny = 0
<br>fourier_nz = 0
<br>pme_order = 4
<br>ewald_rtol = 1e-5
<br>optimize_fft = yes
<br>;
<br>; Energy minimizing stuff
<br>;
<br>emtol = 1000.0
<br>emstep = 0.01<br><br>I could not understand what i did mistake, and where the problem was?<br><br>PLease help me to solve this error<br><br><br>Thank you<br><br>