<pre style="font-family: tahoma,sans-serif;"><font size="4">dear justin <br><br>Fatal error:<br>[ file spc.itp, line 46 ]:<br>Atom index (1) in settles out of bounds (1-0).<br>This probably means that you have inserted topology section "settles"<br>
in a part belonging to a different molecule than you intended to.<br>In that case move the "settles" section to the right molecule.<br><br>I checked topology file and sent topology and spc.itp file. please guide me.</font></pre>
<font size="4">this is my topology file :</font><br><br>; Include forcefield parameters<br>#include "ffamber03.itp"<br><br>; Include chain topologies<br>#include "c_A.itp"<br>#include "c_B.itp"<br>
<br>; Include water topology<br>#include "spc.itp"<br><br>#ifdef POSRES_WATER<br>; Position restraint for each water oxygen<br>[ position_restraints ]<br>; i funct fcx fcy fcz<br> 1 1 1000 1000 1000<br>
#endif<br><br>; Include generic topology for ions<br>#include "ions.itp"<br><br>[ system ]<br>; Name<br>Protein in water<br><br>[ molecules ]<br>; Compound #mols<br>Protein_A 1<br>Protein_B 1<br>
SOL 7127<br><br><font size="4">this is my spc.itp file:</font><br><br>[ moleculetype ]<br>; molname nrexcl<br>SOL 2<br><br>[ atoms ]<br>; nr type resnr residue atom cgnr charge mass<br>
#ifdef _FF_GROMACS <br> 1 OW 1 SOL OW 1 -0.82<br> 2 HW 1 SOL HW1 1 0.41<br> 3 HW 1 SOL HW2 1 0.41<br>#endif<br>#ifdef _FF_GROMOS96 <br>
#ifdef HEAVY_H<br> 1 OW 1 SOL OW 1 -0.82 9.95140<br> 2 H 1 SOL HW1 1 0.41 4.03200<br> 3 H 1 SOL HW2 1 0.41 4.03200<br>#else<br>
1 OW 1 SOL OW 1 -0.82 15.99940<br> 2 H 1 SOL HW1 1 0.41 1.00800<br> 3 H 1 SOL HW2 1 0.41 1.00800<br>#endif<br>#endif<br>
#ifdef _FF_OPLS <br> 1 opls_116 1 SOL OW 1 -0.82 <br> 2 opls_117 1 SOL HW1 1 0.41 <br> 3 opls_117 1 SOL HW2 1 0.41 <br>#endif<br>#ifdef _FF_CHARMM<br>
1 OW 1 SOL OW 1 -0.82<br> 2 HW 1 SOL HW1 1 0.41<br> 3 HW 1 SOL HW2 1 0.41<br>#endif<br><br>#ifdef FLEXIBLE<br>[ bonds ]<br>; i j funct length force.c.<br>
1 2 1 0.1 345000 0.1 345000<br>1 3 1 0.1 345000 0.1 345000<br> <br>[ angles ]<br>; i j k funct angle force.c.<br>2 1 3 1 109.47 383 109.47 383<br>
#else<br>[ settles ]<br>; OW funct doh dhh<br>1 1 0.1 0.16330<br><br>[ exclusions ]<br>1 2 3<br>2 1 3<br>3 1 2<br>#endif<br><br><br>