Dear Gmx-users,<br>I have followed http://folding.stanford.edu/ffamber/ for porting amber in Gromacs and i am trying to simulate protein-DNA complex. Preprocessing the topology files gives error as below:<br><br>Back Off! I just backed up mdout.mdp to ./#mdout.mdp.22#<br>checking input for internal consistency...<br>calling /lib/cpp -traditional...<br>processing topology...<br>Generated 2628 of the 2628 non-bonded parameter combinations<br>Generating 1-4 interactions: fudge = 0.5<br>Generated 2628 of the 2628 1-4 parameter combinations<br>Cleaning up temporary file gromppkzsTQq<br>Fatal error: [ file "/usr/local/gromacs/share/top/spc.itp", line 41 ]:<br> Atom index (1) in settles out of bounds (1-0)<br><br>I checked at the spc.itp file and found that the line 41 is:<br><br> [ settles ]<br> ; OW funct doh
dhh<br> 1 1 0.1 0.16333<br><br><br><br>and i am using em.mdp file:<br>;<br>; User spoel (236)<br>; Wed Nov 3 17:12:44 1993<br>; Input file<br>;<br>cpp = /lib/cpp<br>define = -DFLEX_SPC<br>constraints = none<br>integrator = steep<br>nsteps = 100<br>;<br>; Energy minimizing
stuff<br>;<br>emtol = 2000<br>emstep = 0.01<br><br>nstcomm = 1<br>ns_type = grid<br>rlist = 1<br>rcoulomb = 1.0<br>rvdw = 1.0<br>Tcoupl = no<br>Pcoupl =
no<br>gen_vel = no<br><br>I tried the earlier post suggestion: that "include spc.itp " line must be before the "[molecule] section", but still gives the same error as:<br> <br>Fatal error: [ file "/usr/local/gromacs/share/top/spc.itp", line 41 ]:<br> Atom index (1) in settles out of bounds (1-0)<br><br>Thanks and regards<br>-Alaguraj.V<br><BR><BR>ALAGURAJ VELUCHAMY<br>c/o Dr.S.KRISHNASWAMY,<br>CENTRE OF EXCELLENCE IN BIOINFORMATICS,<br>MADURAI KAMARAJ UNIVERSITY,<br>MADURAI, TN.<br>Ph:09486148690<p> 
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