<div>Hi,</div>
<div>With my grompp.mdp,topol.top and gonf.gro i gave the command and the output was</div>
<div>[abhijit@SCFBioServer gromacs]$ grompp -f grompp.mdp -p topol.top -c conf.gro -o water.tpr<br> :-) G R O M A C S (-:</div>
<p> Gravel Rubs Often Many Awfully Cauterized Sores</p>
<p> :-) VERSION 4.0.4 (-:</p>
<p><br> Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.<br> Copyright (c) 1991-2000, University of Groningen, The Netherlands.<br> Copyright (c) 2001-2008, The GROMACS development team,<br>
check out <a href="http://www.gromacs.org/">http://www.gromacs.org</a> for more information.</p>
<p> This program is free software; you can redistribute it and/or<br> modify it under the terms of the GNU General Public License<br> as published by the Free Software Foundation; either version 2<br>
of the License, or (at your option) any later version.</p>
<p> :-) grompp (-:</p>
<p>Option Filename Type Description<br>------------------------------------------------------------<br> -f grompp.mdp Input, Opt! grompp input file with MD parameters<br> -po mdout.mdp Output grompp input file with MD parameters<br>
-c conf.gro Input Structure file: gro g96 pdb tpr tpb tpa<br> -r conf.gro Input, Opt. Structure file: gro g96 pdb tpr tpb tpa<br> -rb conf.gro Input, Opt. Structure file: gro g96 pdb tpr tpb tpa<br>
-n index.ndx Input, Opt. Index file<br> -p topol.top Input Topology file<br> -pp processed.top Output, Opt. Topology file<br> -o water.tpr Output Run input file: tpr tpb tpa<br> -t traj.trr Input, Opt. Full precision trajectory: trr trj cpt<br>
-e ener.edr Input, Opt. Energy file: edr ene</p>
<p>Option Type Value Description<br>------------------------------------------------------<br>-[no]h bool no Print help info and quit<br>-nice int 0 Set the nicelevel<br>-[no]v bool yes Be loud and noisy<br>
-time real -1 Take frame at or first after this time.<br>-[no]rmvsbds bool yes Remove constant bonded interactions with virtual<br> sites<br>-maxwarn int 0 Number of allowed warnings during input processing<br>
-[no]zero bool no Set parameters for bonded interactions without<br> defaults to zero instead of generating an error<br>-[no]renum bool yes Renumber atomtypes and minimize number of<br>
atomtypes</p>
<p>Ignoring obsolete mdp entry 'cpp'<br>checking input for internal consistency...</p>
<p>NOTE 1 [file grompp.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.</p>
<p>processing topology...</p>
<p>-------------------------------------------------------<br>Program grompp, VERSION 4.0.4<br>Source code file: topio.c, line: 415</p>
<p>Fatal error:<br>Syntax error - File topol.top, line 4<br>Last line read:<br>'[ atomtypes ]'<br>Invalid order for directive atomtypes<br>-------------------------------------------------------</p>
<p>"I believe in miracles cause I'm one" (The Ramones)</p>
<div>[abhijit@SCFBioServer gromacs]$</div>
<div> my topol.top file is </div>
<div>xirs fudgeLJ fudgeQQ<br>1 2 yes 0.5 0.5</div>
<div>[ atomtypes ]<br>;name at.num mass charge ptype sigma epsilon<br> OW 8 15.99940 0.000 A 0.3166 0.65<br> HW 1 1.00800 0.000 A 0.00000E+00 0.00000E+00</div>
<div><br>;---------------------------------------------------------------<br>; Definition of the SPC/E water model---------------------------<br>;<br>[ moleculetype ]<br>; molname nrexcl<br>SOL 2</div>
<div>[ atoms ]<br>; nr type resnr residue atom cgnr charge mass<br> 1 OW 1 SOL OW 1 -0.8476<br> 2 HW 1 SOL HW1 1 0.4238<br> 3 HW 1 SOL HW2 1 0.4238</div>
<div>[ settles ]<br>; OW funct doh dhh<br>1 1 0.1 0.16330</div>
<div>[ exclusions ]<br>1 2 3<br>2 1 3<br>3 1 2</div>
<div>;---------------------------------------------------------------<br>; End of definition of the SPC/E water model--------------------<br>;---------------------------------------------------------------</div>
<div><br>[ system ]<br>Water SPC/E</div>
<div>[ molecules ]<br>SOL 216</div>
<div><br>the conf.gro file is </div>
<div> 203SOL HW1 608 1.821 0.322 0.817 0.8928 1.1548 0.7389<br> 203SOL HW2 609 1.875 0.440 0.718 -1.9604 0.3767 -1.7905<br> 204SOL OW 610 0.779 1.345 0.916 0.2112 -0.0070 0.2315<br>
204SOL HW1 611 0.686 1.338 0.954 0.8109 -1.6887 1.4414<br> 204SOL HW2 612 0.805 1.442 0.909 -2.0435 0.5275 -1.1795<br> 205SOL OW 613 1.718 1.114 0.507 0.2154 -0.1127 -0.1792<br> 205SOL HW1 614 1.755 1.098 0.416 -0.9406 -0.2600 -0.6191<br>
205SOL HW2 615 1.769 1.060 0.574 -1.8561 -3.6296 -1.3196<br> 206SOL OW 616 0.694 0.641 1.677 0.0172 0.0058 -0.2012<br> 206SOL HW1 617 0.784 0.654 1.717 1.2820 -2.2353 -2.2392<br> 206SOL HW2 618 0.647 0.566 1.723 -1.1125 1.6018 1.2995<br>
207SOL OW 619 1.089 0.525 0.672 0.1215 -0.1196 -0.1599<br> 207SOL HW1 620 1.124 0.538 0.579 0.9751 2.2078 0.4622<br> 207SOL HW2 621 0.995 0.490 0.668 -1.9486 5.2441 -2.0093<br> 208SOL OW 622 1.644 0.521 0.536 0.8695 -0.0305 0.4538<br>
208SOL HW1 623 1.568 0.521 0.602 1.0461 -0.1378 0.6487<br> 208SOL HW2 624 1.683 0.429 0.530 0.6027 -0.1103 -0.0867<br> 209SOL OW 625 1.607 0.804 1.136 0.1924 -0.0775 -0.0451<br> 209SOL HW1 626 1.700 0.841 1.138 -0.3765 1.4071 -1.2113<br>
209SOL HW2 627 1.602 0.725 1.198 1.8134 0.8052 1.2429<br> 210SOL OW 628 0.961 1.176 0.727 0.0667 0.1065 0.0824<br> 210SOL HW1 629 0.878 1.218 0.765 0.0936 -0.8745 1.2584<br> 210SOL HW2 630 0.959 1.078 0.744 0.3982 -0.2571 -1.9273<br>
211SOL OW 631 1.441 1.835 1.811 0.4461 -0.3668 -0.0023<br> 211SOL HW1 632 1.478 1.796 1.727 -1.1085 -1.3547 -0.2480<br> 211SOL HW2 633 1.442 1.766 1.884 -1.2578 -0.5603 -0.1372<br> 212SOL OW 634 0.594 0.650 0.961 0.1032 0.4852 0.5329<br>
212SOL HW1 635 0.642 0.644 1.049 0.6450 -0.1007 0.1907<br> 212SOL HW2 636 0.660 0.659 0.887 -0.3688 1.3618 0.2061<br> 213SOL OW 637 1.227 1.503 0.161 -0.0292 -0.8161 0.3425<br> 213SOL HW1 638 1.225 1.458 0.251 0.3570 -0.7808 0.3667<br>
213SOL HW2 639 1.136 1.535 0.138 -0.2322 -1.2929 0.4912<br> 214SOL OW 640 0.606 0.647 1.408 -0.1516 -0.3989 0.3259<br> 214SOL HW1 641 0.639 0.672 1.499 -1.3540 1.1041 0.3654<br> 214SOL HW2 642 0.591 0.548 1.404 2.9386 -0.9536 0.7368<br>
215SOL OW 643 1.607 1.679 0.596 0.1020 -0.0876 0.2788<br> 215SOL HW1 644 1.558 1.743 0.537 -1.2519 -2.7009 -1.5800<br> 215SOL HW2 645 1.542 1.635 0.658 0.9367 0.0657 1.2497<br> 216SOL OW 646 1.663 1.409 0.500 0.3668 0.1318 0.2586<br>
216SOL HW1 647 1.652 1.490 0.558 0.1481 1.3472 -1.4439<br> 216SOL HW2 648 1.644 1.327 0.554 0.0397 1.2345 1.8708<br> 1.85058 1.85058 1.85058<br>and thegrompp.mdpo file is </div>
<div>tc-grps = System<br>tau_t = 0.1<br>ref_t = 300</div>
<div>Pcoupl = No</div>
<div>gen_vel = yes<br>gen_temp = 300<br>gen_seed = 1993</div>
<div>PCE model<br>cpp = /usr/bin/cpp<br>include =<br>define =</div>
<div>integrator = md<br>dt = 0.001<br>nsteps = 50000</div>
<div>nstxtcout = 100<br>xtc-precision = 1000</div>
<div>rlist = 0.9</div>
<div>coulombtype = Cut-off<br>rcoulomb = 0.9</div>
<div>vdw-type = Cut-off<br>rvdw = 0.9</div>
<div>DispCorr = EnerPres</div>
<div>Tcoupl = berendsen<br>tc-grps = System<br>tau_t = 0.1<br>ref_t = 300</div>
<div>Pcoupl = No</div>
<div>gen_vel = yes<br>gen_temp = 300<br>gen_seed = 1993:x<br> so what is the problem</div>
<div> Abhijit Kayal<br></div>