Hello
I am having trouble running a dimmer invacuo simulation. I can do energy
minimization on it, but when I attempt to generate md.tpr file I get this weird
message about “Group Protein not found in index”. I don’t see why I would need
an index file. I have no trouble generating a md.tpr
Hello
I am just trying to do a simple MD on a dimmer system (in which the dimmers are
NOT identical). I can use pdb2gmx to create a topology file and four .itp
files pores.chainA.itp, pores.chainX.itp; system.Protein.chainA.itp and
system.Protein.chainX.itp.
When I use grompp however, I
Hi Justin
Thanks for your response. Here are the files you asked for. They are all text
files. I am still attempting to fix this, but am still getting the error I
described no matter what I have done so far.
Thanks again,
Stevegrompp -f pr.mdp -n pr.ndx -c prbox.pdb -p system.top -o pr.tpr
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