<html><head><style type="text/css"><!-- DIV {margin:0px;} --></style></head><body><div style="font-family:times new roman,new york,times,serif;font-size:12pt;color:#000000;"><div>Dear All,<br><br>I am trying to add a single strand dna, and single walled carbon nanotube in a box using the genbox command. After typing following command: <br><br>genbox -cp cntcapped.pdb -cs spc216.gro -ci ssgcg.gro -nmol 1 -box 2 2 2 -o cntdna.gro, <br><br>I get: Reading solute configuration<br><br>Containing 168 atoms in 1 residues<br>Initialising van der waals distances...<br><br>WARNING: masses and atomic (Van der Waals) radii will be determined<br> based on residue and atom names. These numbers can deviate<br> from the correct mass and radius of the atom type.<br><br>Reading solvent configuration<br>"Giving Russians Opium May Alter Current Situation"<br>solvent configuration
contains 648 atoms in 216 residues<br><br><br>and then it takes forever to produce output. <br><br>I tried to generate an output with just one molecule in solvent (spc216.gro), and I ran into same problem. I suspect something is wrong with my solvent input (file attached). I copied this file from gromacs/tutor/water folder, though it looks reasonable when I view I view the corresponding .pdb file in rasmol (I created .gro file from .pdb file using editconf -f spc216.pdb -o spc216.gro). <br><br>Could anyone please guide me about possible issues, and how to resolve them? <br><br>Thank You,<br>Majid<br><br><br></div>
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