[gmx-users] grompp: no such moleculetype

[Justin A. Lemkul]

Francesco Pietra wrote:
> Hi:
> 
> As I found it difficult to manage solvation - the way I would like -
> with a pore protein (a trimer) partly immersed into a bilayer, I
> started with the protein alone in vacuum, in order to try to fix the
> problems step-by-step. Unfortunately, I can't fix simple problems with
> grompp.
> 
> 1) Generated mod21.itp from mod21.pdb
> 
> 2) Generated mod21.cg.pdb with awk script)
> 
> 3) editconf -f mod21.cg.pdb -o mod21.cg.gro
> 
> 4) genbox -cp mod21.cg.gro -box 10 17 10 -o mod21.cg.box.gro
> 
> 5) grompp -np 4 -f mod21.cg.box.mdp  -c mod21.cg.box.gro -p
> mod21.cg.box.top -warnmax 10
> 
>    Error: no such moleculetype Protein.
> 
> .............................
> .mdp is merely a renamed martini_v2.0.example.mdp, taking care that
> "cpp  = /usr/bin/cpp".
> 
> .top was from editing martini_v2.0.example.top and reads (in between ===):
> ======
> ;
> ; mod21 | MARTINI 2.1
> ;
> 
> ; Include force field parameters containing all particle definitions,
> ; the interaction matrix, plus the topology for water.
> 
> #include "martini_v2.1.itp"
> 
> ; Then include the file(s) containing the topologies of other
> ; molecules present in your system.
> 
> ; #include "martini_v2.0_lipids.itp"
> ; #include "martini_v2.0_salt.itp"
> 
> #include mod21.itp
> 

This #include statement has the wrong syntax.  See any of the above for the 
correct way to do it.

-Justin

-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
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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