[gmx-users] RE:problem regarding .top file generated by genbox
sudheer babu
sudheer.pbm07 at gmail.com
Tue Feb 19 07:23:14 CET 2008
Thanks for your reply Mr.justin
i am sending the commands and .itp file sequence
the command i have used for protein insertion into membrane is
genbox -cs lipid.gro -cp protein.gro -p topol.top -o popc_protein.gro , this
command was fine it ran without error.
Later
grompp -f em.mdp -c popc_protein.gro(generated by genbox) -p
topol.top(generated by genbox) -o
em.tpr
when i ran this grompp command its showing that atom typr NR, HC, CR1 not
found
i am pasting part of my topology file
This is your topology file
; "Move Over Hogey Bear" (Urban Dance Squad)
;
; Include forcefield parameters
#include "ffgmx.itp"
#include "lipid.itp"
#include "popc.itp
17 N 3 HISH N 7 -0.28 14.0067 ; qtot
0.72
18 H 3 HISH H 7 0.28 1.008 ; qtot
1
19 CH1 3 HISH CA 8 0 13.019 ; qtot
1
20 CH2 3 HISH CB 8 0 14.027 ; qtot
1
21 C 3 HISH CG 9 -0.05 12.011 ; qtot
0.95
22 NR 3 HISH ND1 9 0.38 14.0067 ; qtot
1.33
23 H 3 HISH HD1 9 0.3 1.008 ; qtot
1.63
24 CR1 3 HISH CD2 9 0 13.019 ; qtot
1.63
25 CR1 3 HISH CE1 9 -0.24 13.019 ; qtot
1.39
26 NR 3 HISH NE2 9 0.31 14.0067 ; qtot
1.7
27 H 3 HISH HE2 9 0.3 1.008 ; qtot
2
28 C 3 HISH C 10 0.38 12.011 ; qtot
2.38
29 O 3 HISH O 10 -0.38 15.9994 ; qtot
2
30 N 4 HISH N 11 -0.28 14.0067 ; qtot
1.72
31 H 4 HISH H 11 0.28 1.008 ; qtot
2
32 CH1 4 HISH CA 12 0 13.019 ; qtot
2
33 CH2 4 HISH CB 12 0 14.027 ; qtot
2
34 C 4 HISH CG 13 -0.05 12.011 ; qtot
1.95
35 NR 4 HISH ND1 13 0.38 14.0067 ; qtot
2.33
36 H 4 HISH HD1 13 0.3 1.008 ; qtot
2.63
37 CR1 4 HISH CD2 13 0 13.019 ; qtot
2.63
38 CR1 4 HISH CE1 13 -0.24 13.019 ; qtot
2.39
39 NR 4 HISH NE2 13 0.31 14.0067 ; qtot
2.7
40 H 4 HISH HE2 13 0.3 1.008 ; qtot
3
41 C 4 HISH C 14 0.38 12.011 ; qtot
3.38
42 O 4 HISH O 14 -0.38 15.9994 ; qtot
3
366 N 41 PHE N 160 -0.28 14.0067 ; qtot
2.72
367 H 41 PHE H 160 0.28 1.008 ; qtot
3
368 CH1 41 PHE CA 161 0 13.019 ; qtot
3
369 CH2 41 PHE CB 161 0 14.027 ; qtot
3
370 C 41 PHE CG 161 0 12.011 ; qtot
3
371 C 41 PHE CD1 162 -0.1 12.011 ; qtot
2.9
372 HC 41 PHE HD1 162 0.1 1.008 ; qtot
3
373 C 41 PHE CD2 163 -0.1 12.011 ; qtot
2.9
374 HC 41 PHE HD2 163 0.1 1.008 ; qtot
3
375 C 41 PHE CE1 164 -0.1 12.011 ; qtot
2.9
376 HC 41 PHE HE1 164 0.1 1.008 ; qtot
3
377 C 41 PHE CE2 165 -0.1 12.011 ; qtot
2.9
378 HC 41 PHE HE2 165 0.1 1.008 ; qtot
3
379 C 41 PHE CZ 166 -0.1 12.011 ; qtot
2.9
380 HC 41 PHE HZ 166 0.1 1.008 ; qtot
3
381 C 41 PHE C 167 0.38 12.011 ; qtot
3.38
382 O 41 PHE O 167 -0.38 15.9994 ; qtot
3
; Include Position restraint file
#ifdef POSRES
#include "posre.itp"
#endif
; Include water topology
#include "spc.itp"
#ifdef POSRES_WATER
; Position restraint for each water oxygen
[ position_restraints ]
; i funct fcx fcy fcz
1 1 1000 1000 1000
#endif
; Include generic topology for ions
#include "ions.itp"
[ system ]
; Name
protein in popc in water
[ molecules ]
; Compound #mols
Protein 1
POPC 98
CL- 3
SOL 2457
Thanks in advance.
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