Please copy and paste in here the contents of your .top file.
Catch ya, Dr. Dallas Warren Medicinal Chemistry and Drug Action Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 [email protected] +61 3 9903 9304 --------------------------------- When the only tool you own is a hammer, every problem begins to resemble a nail. From: [email protected] [mailto:[email protected]] On Behalf Of mustafa bilsel Sent: Friday, 7 January 2011 12:32 PM To: [email protected] Subject: [gmx-users] methanol simulation error Hi all, I try to make a simulation in methanol. I use gromos43a1 forcefield. My command follow, pdb2gmx -f xxx.pdb editconf -f conf.gro -bt dodecahedron -d 0.8 -o box.gro genbox -cp box.gro -cs methanol216.gro -p topol.top -o solvated.gro When grompp for minimization it gives an error: Atomtype CMET not found I have used grep to count the methanol molecules and added SOL 660 comment in .top file to tell the number of methanols. Also I added #include "gromos43a1.ff/methanol.itp" line to .top. Please don't suggest non-water solvation in how-to part of Gromacs web. Could you tell me what missing is? best wishes mustafa
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