Hi Moeed,<br><br>Hello, I use to encounter the same error and I fix it by modifying the index file (.ndx). Maybe you have re-define the group name in your topology file. You can have a check on the .ndx file and see if <b>protein </b>has been included. I do it like first,<br>
<br>make_ndx -f *.gro -o *.ndx <br><br>then modify it by command or manually change the content of *.ndx file.<br><br>Hope this could help, good luck.<br><br>Best,<br><br>Xi<br><br><div class="gmail_quote">2010/4/25 Moeed <span dir="ltr"><<a href="mailto:lecielll@googlemail.com">lecielll@googlemail.com</a>></span><br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">I would be most thankful if you could help me warning 1, note 1 and thr
fatal error. I I read about -n option but I dont know where in command
line i have to include it. Thank you.<br><br>
<pre style="text-align: justify;" lang="en-US">grompp -f pr -c Hexane_b4pr.gro -r Hexane_b4pr.gro -p HexaneModified-Residuename.top -o Hexane_pr >& output.grompp_pr</pre>
<br>output file:<br><pre style="text-align: justify;" lang="en-US">output.grompp_pr<br></pre><br><b>WARNING 1 [file pr.mdp, line unknown]:<br> Unknown or double left-hand 'warnings' in parameter file</b><br><br>
<br>checking input for internal consistency...<br><br><b>NOTE 1 [file pr.mdp, line unknown]:<br>
The Berendsen thermostat does not generate the correct kinetic energy<br> distribution. You might want to consider using the V-rescale thermostat.</b><br><br>Opening library file /chem_soft/gromacs/share/<div>
gromacs/top/ffoplsaa.itp<br>
Opening library file /chem_soft/gromacs/share/gromacs/top/ffoplsaanb.itp<br>Opening library file /chem_soft/gromacs/share/gromacs/top/ffoplsaabon.itp<br>Generated 332520 of the 332520 non-bonded parameter combinations<br>
Generating 1-4 interactions: fudge = 0.5<br>Generated 332520 of the 332520 1-4 parameter combinations<br>Excluding 3 bonded neighbours molecule type 'HEX'<br>processing coordinates...<br>double-checking input for internal consistency...<br>
Velocities were taken from a Maxwell distribution at 300 K<br>renumbering atomtypes...<br>converting bonded parameters...<br><br>NOTE 2 [file HexaneModified-Residuename.top, line unknown]:<br> The largest charge group contains 20 atoms.<br>
Since atoms only see each other when the centers of geometry of the charge<br> groups they belong to are within the cut-off distance, too large charge<br> groups can lead to serious cut-off artifacts.<br> For efficiency and accuracy, charge group should consist of a few atoms.<br>
For all-atom force fields use: CH3, CH2, CH, NH2, NH, OH, CO2, CO, etc.<br><br>initialising group options...<br>processing index file...<br>Opening library file /chem_soft/gromacs/share/gromacs/top/aminoacids.dat<br><br>
-------------------------------------------------------<br>Program grompp, VERSION 4.0.7<br>Source code file: readir.c, line: 1007<br><br><b>Fatal error:<br>Group protein not found in indexfile.<br>Maybe you have non-default goups in your mdp file, while not using the '-n' option of grompp.<br>
In that case use the '-n' option.<br></b><br>-------------------------------------------------------<br>pr.mdp file:*************************************************************<br><br><br>warnings = 10<br>
cpp = /lib/cpp<br>define = -DPOSRES<br>constraints = all-bonds<br>integrator = md<br>dt = 0.002 ; ps !<br>nsteps = 500 ; total 1.0 ps.<br>
nstcomm = 1<br>nstxout = 10<br>nstvout = 1000<br>nstfout = 0<br>nstlog = 10<br>nstenergy = 10<br>nstlist = 10<br>ns_type = grid<br>
rlist = 1.0<br>rcoulomb = 1.0<br>rvdw = 1.0<br>; Berendsen temperature coupling is on in two groups<br>Tcoupl = berendsen<br>tau_t = 0.1 0.1<br>
tc-grps = protein sol<br>ref_t = 300 300<br>; Pressure coupling is not on<br>Pcoupl = no<br>tau_p = 0.5<br>compressibility = 4.5e-5<br>ref_p = 1.0<br>
; Generate velocites is on at 300 K.<br>gen_vel = yes<br>gen_temp = 300.0<br>gen_seed = 173529</div><input type="hidden"><input type="hidden"><div>
</div>
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