[gmx-users] methanol simulation error

Dallas Warren Dallas.Warren at monash.edu
Fri Jan 7 02:42:38 CET 2011

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
dallas.warren at monash.edu

+61 3 9903 9304
When the only tool you own is a hammer, every problem begins to resemble
a nail. 


From: gmx-users-bounces at gromacs.org
[mailto:gmx-users-bounces at gromacs.org] On Behalf Of mustafa bilsel
Sent: Friday, 7 January 2011 12:32 PM
To: gmx-users at gromacs.org
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

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