Hi there, in special Berk.<div><br></div><div>So pdb2gmx may be working with HIS and variants for oplsaa but now, something that was working before is failing:</div><div><br></div><div><div>wget -c &quot;<a href="http://www.pdbe.org/download/1BNA">http://www.pdbe.org/download/1BNA</a>&quot; -O 1BNA.pdb</div>

<div>grep &#39;ATOM  &#39; 1BNA.pdb &gt;| DNA.pdb</div><div><br></div><div><div>cat &lt;&lt; EOF &gt;| SPE.mdp</div><div>define = -DFLEXIBLE</div><div>integrator               = md</div><div>nsteps                   = 0</div>

<div>dt                       = 0.001</div><div>constraints              = none</div><div>emtol                    = 10.0</div><div>emstep                   = 0.01</div><div>nstcomm                  = 1</div><div>ns_type                  = simple</div>

<div>nstlist                  = 0</div><div>rlist                    = 0</div><div>rcoulomb                 = 0</div><div>rvdw                     = 0</div><div>Tcoupl                   = no</div><div>Pcoupl                   = no</div>

<div>gen_vel                  = no</div><div>nstxout                  = 1</div><div>pbc                      = no</div><div>nstlog = 1</div><div>nstenergy = 1</div><div>nstvout = 1</div><div>nstfout = 1</div><div>nstxtcout = 1</div>

<div>comm_mode = ANGULAR</div><div>continuation = yes</div><div>EOF</div></div><div><br></div><div><div>pdb2gmx -f DNA.pdb -o DnaAmberSBGMX45.pdb -ff amber99sb -water none -p DnaAmberSBGMX45</div><div>[snip]</div></div><div>

<div>8 out of 8 lines of specbond.dat converted successfully</div><div>[1]    42209 segmentation fault  pdb2gmx -f DNA.pdb -o DnaAmberSBGMX45.pdb -ff amber99sb -water none -p </div><div><br></div></div>with 5e347 it worded fine, i.e, it opens files</div>

<div><br></div><div><div>Opening force field file /Volumes/CloneAmadeus/usr/local/share/gromacs/top/amber99sb.ff/aminoacids.arn</div><div>Opening force field file /Volumes/CloneAmadeus/usr/local/share/gromacs/top/amber99sb.ff/dna.arn</div>

<div>Opening force field file /Volumes/CloneAmadeus/usr/local/share/gromacs/top/amber99sb.ff/rna.arn</div></div><div><br></div><div>and proceed.</div><div><br></div><div>Alan<br>-- <br>Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate<br>

Department of Biochemistry, University of Cambridge. <br>80 Tennis Court Road, Cambridge CB2 1GA, UK.<br>&gt;&gt;<a href="http://www.bio.cam.ac.uk/~awd28">http://www.bio.cam.ac.uk/~awd28</a>&lt;&lt;<br>
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