Hi there, in special Berk. So pdb2gmx may be working with HIS and variants for oplsaa but now, something that was working before is failing:
wget -c "http://www.pdbe.org/download/1BNA"; -O 1BNA.pdb grep 'ATOM ' 1BNA.pdb >| DNA.pdb cat << EOF >| SPE.mdp define = -DFLEXIBLE integrator = md nsteps = 0 dt = 0.001 constraints = none emtol = 10.0 emstep = 0.01 nstcomm = 1 ns_type = simple nstlist = 0 rlist = 0 rcoulomb = 0 rvdw = 0 Tcoupl = no Pcoupl = no gen_vel = no nstxout = 1 pbc = no nstlog = 1 nstenergy = 1 nstvout = 1 nstfout = 1 nstxtcout = 1 comm_mode = ANGULAR continuation = yes EOF pdb2gmx -f DNA.pdb -o DnaAmberSBGMX45.pdb -ff amber99sb -water none -p DnaAmberSBGMX45 [snip] 8 out of 8 lines of specbond.dat converted successfully [1] 42209 segmentation fault pdb2gmx -f DNA.pdb -o DnaAmberSBGMX45.pdb -ff amber99sb -water none -p with 5e347 it worded fine, i.e, it opens files Opening force field file /Volumes/CloneAmadeus/usr/local/share/gromacs/top/amber99sb.ff/aminoacids.arn Opening force field file /Volumes/CloneAmadeus/usr/local/share/gromacs/top/amber99sb.ff/dna.arn Opening force field file /Volumes/CloneAmadeus/usr/local/share/gromacs/top/amber99sb.ff/rna.arn and proceed. Alan -- Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate Department of Biochemistry, University of Cambridge. 80 Tennis Court Road, Cambridge CB2 1GA, UK. >>http://www.bio.cam.ac.uk/~awd28<<
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