mustafa bilsel wrote:
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 will assume you're not using the current version of Gromacs. This was a bug
that was fixed some time ago. Please upgrade to version 4.5.3.
I have used grep to count the methanol molecules and added SOL 660
comment in .top file to tell the number of methanols.
Is SOL the appropriate name given in the [moleculetype] directive for methanol?
The name "SOL" is the default name for water in Gromacs, so this may be where
you're having problems. Just because methanol is a solvent doesn't mean it
should be named SOL. Check the name in the topology to be sure this is what you
should be using.
-Justin
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
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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