[gmx-users] grompp: no such moleculetype

[Francesco Pietra]

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