Dear all, I tried to send this message earlier, but I had attached a pdb file and apparently it exceeded the size allowed in the mailing list and is awinting for the list moderator to evaluate it. I apologize if the message is sent twice.
I am trying to solvate a protein in a box of acetonitrile using genbox. My initial solvent box is a cubic box containing 300 molecules of acetonitrile that has been equilibrated for 500 ps at constant P and T. I used the following protocol to generate the box: ####################################################################################### #create the box editconf -f protein.pdb -d 1.2 -o protein_in_box.pdb -bt dodecahedron #solvate genbox -cp protein_in_box.pdb -cs acetonitrile_eq.gro -o protein_in_acetonitrile.gro #convert the box to visualize it touch empty.mdp grompp -f empty.mdp -c protein_in_acetonitrile.gro -p 01_make_top/protein_ACN.top trjconv -f protein_in_acetonitrile.gro -o protein_in_acetonitrile.pdb -pbc atom -ur compact <<EOF 0 EOF ####################################################################################### After these steps I get a box that has holes and I can't understand why. I couldn't send the final pdb file in attachment, if anyone thinks he/she can help and whishes to see the pdb file I will send it to your email. Thanks in advance. Diana -- Diana Lousa PhD student Protein Modeling Laboratory ITQB/UNL Oeiras, Portugal
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