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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