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
; Define a name for your system
[ system ]
mod21
; Define the composition of your system
; The molecule names should correspond to those defined in the itp file(s).
[ molecules ]
Protein 1
; DPPC 128
; W 2000
; NA+ 20
; CL- 20
===========
Correspondingly, mod21.cg.box.gro reads:
=========
Great Red Oystrich Makes All Chemists Sane
2875
1LEU BN0 1 15.604 6.397 9.477
1LEU SC1 2 15.848 6.475 9.463
2SER BN0 3 15.784 6.086 9.582
2SER SC1 4 15.874 6.060 9.703
...........................
............................
1270TYR BN0 2872 14.759 6.270 10.494
1270TYR SC1 2873 14.668 6.105 10.342
1270TYR SC2 2874 14.442 6.038 10.300
1270TYR SC3 2875 14.607 5.874 10.352
10.00000 17.00000 10.00000
=========
and mod21.itp file reads:
====
;;; MARTINI 2.1 coarse-grained topology
;;; Generated by seq2itp.pl version 1.1.2
;;; SEQ: LSLKRALWAL ................
.............................
[moleculetype]
;molname exclusions
Protein 1
[atoms]
1 Qd 1 LEU BCQd 1 1.000 ; COI
2 AC1 1 LEU SCAC1 2 0.000 ; COI
.......................
.......................
[ bonds ]
;backbone-backbone bonds
1 3 1 0.350 400 ; COI-COI
..........................
.......................
2871 2872 1 0.350 400 ; HLX-COI
;backbone-sidechain bonds
1 2 1 0.330 7500 ; LEU1
.......................
...................
2872 2873 1 0.320 5000 ; TYR1270
;sc1-sc2 bonds (ARG, LYS)
8 9 1 0.280 5000 ; LYS4
..............................
...............................
2806 2807 1 0.280 5000 ; LYS1236
;short elastic bonds
85 91 1 0.640 2500 ; HIS35-THR37
...........................
..............................
2800 2805 1 0.640 2500 ; GLN1234-LYS1236
;long elastic bonds
85 93 1 0.970 2500 ; HIS35-LYS38
......................
........................
2798 2805 1 0.970 2500 ; GLU1233-LYS1236
[ constraints ]
;sc-sc constraints (Ring Structures)
17 18 1 0.270 ; TRP8
............................
............................
2874 2875 1 0.270 ; TYR1270
;bc-sc constraints (ITV)
38 39 1 0.265 ; VAL18
....................
.................
2853 2854 1 0.265 ; VAL1262
[angles]
;backbone-backbone-backbone angles
1 3 5 2 127.00 25 ; COI-COI-BND
.......................
......................
2867 2871 2872 2 96.00 700 ; HLX-HLX-COI
;backbone-backbone-sidechain angles
3 1 2 2 100.00 25 ; COI-LEU1
......................
.......................
2871 2872 2873 2 100.00 25 ; HLX-TYR1270
;backbone-sidechain-sidechain angles (ARG and RINGS)
7 8 9 2 180.00 25 ; LYS4
..................
...............
2872 2873 2875 2 150.00 50 ; TYR1270
[dihedrals]
;improper dihedral angles
16 18 19 17 2 0.00 50 ; TRP8
.................
............
2872 2874 2875 2873 2 0.00 50 ; TYR1270
;proper dihedral angles
;helix backbone dihedrals
13 14 16 21 1 -120.00 400 1 ; LEU7
...............
..............
2859 2861 2865 2867 1 -120.00 400 1 ; PHE1266
2861 2865 2867 2871 1 -120.00 400 1 ; ASP1267
============================
I am aware that the structure file .gro should match the topology .top
file with respect to atom names, though I do not understand the error
message above.
Thanks for help
francesco pietra
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