fulya caglar wrote:
Hi Mark,
I'm so sorry for taking so much of your time.I tried to explain how I
generated the sections:
Firstly I named my ligand (protein) files as *drg* and my protein
files as *trp.*
Next I generated the drg.itp and trp.top files with pdb2gmx
pdb2gmx -ff gmx -f drg.pdb -o drg2 -p drg.top
pdb2gmx -ff gmx -f trp.pdb -o trp2.pdb -p trp.top -merge -ignh –ss
Then I pasted the coordinates from drg.pdb onto the end of the trp2.file
and I edited trp.top file; I added #include “ drg.itp” and under the
[molecules] section my ligand.
pdb2gmx doesn't make .itp files, like I said two emails ago.
Mark
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