* TOP FILE (CYCLODEXTRINE) (topol.top) generated by PRODRG
; Include forcefield parameters
#include "ffG43a1.itp"
[ moleculetype ]
; Name nrexcl
UNK 3
[ atoms ]
; nr type resnr resid atom cgnr charge mass
1 OA 1 UNK O2 1 -0.227 15.9994
2 H 1 UNK H22 1 0.027 1.0080
3 CH1 1 UNK C2 1 0.107 13.0190
4 CH1 1 UNK C3 1 0.107 13.0190
5 OA 1 UNK O3 1 -0.227 15.9994
6 H 1 UNK H32 1 0.027 1.0080
7 CH1 1 UNK C4 1 0.186 13.0190
8 OA 1 UNK O4 2 -0.164 15.9994
9 CH1 1 UNK C5 2 0.261 13.0190
10 CH2 1 UNK C6 2 0.104 14.0270
11 OA 1 UNK O6 2 -0.171 15.9994
12 H 1 UNK H69 2 0.036 1.0080
13 OA 1 UNK O5 2 -0.163 15.9994
14 CH1 1 UNK C1 2 0.261 13.0190
15 OA 1 UNK O1 2 -0.164 15.9994
16 CH1 1 UNK CAJ 3 0.199 13.0190
17 CH1 1 UNK CAK 3 0.199 13.0190
18 OA 1 UNK OBY 3 -0.206 15.9994
19 CH2 1 UNK CAL 3 0.065 14.0270
20 OA 1 UNK OBZ 3 -0.215 15.9994
..
..
; Include Position restraint file
#ifdef POSRES
#include "posre.itp"
#endif
; Include ligand topology
#include "drg.itp"
; Include water topology
#include "spc.itp"
[ molecules ]
; Compound #mols
UNK 1
LIG 1
SOL 1682
* ITP FILE ( SULFAMIDE ) (drg.itp) generated by PRODRG
[ moleculetype ]
; Name nrexcl
LIG 3
[ atoms ]
; nr type resnr resid atom cgnr charge mass
1 O 1 LIG O1 1 -0.695 15.9994
2 C 1 LIG C8 1 0.361 12.0110
3 OA 1 LIG O 1 -0.199 15.9994
4 CH1 1 LIG C7 1 0.207 14.0270
5 CH2 1 LIG C6 1 0.044 14.0270
6 NR 1 LIG N1 1 0.011 14.0067
7 SDMSO 1 LIG S 1 2.271 32.0600
8 OM 1 LIG O2 2 -1.000 15.9994
9 OM 1 LIG O3 2 -1.000 15.9994
10 N 1 LIG N 3 0.108 14.0067
11 H 1 LIG H2 3 -0.026 1.0080
12 C 1 LIG C2 3 0.109 12.0110
13 CR1 1 LIG C1 3 -0.034 12.0110
14 HC 1 LIG H1 3 -0.004 1.0080
15 CR1 1 LIG C 3 -0.034 12.0110
16 HC 1 LIG H 3 -0.004 1.0080
17 CR1 1 LIG C5 3 -0.034 12.0110
18 HC 1 LIG H5 3 -0.004 1.0080
19 CR1 1 LIG C4 3 -0.035 12.0110
20 HC 1 LIG H4 3 -0.004 1.0080
21 CR1 1 LIG C3 3 -0.034 12.0110
22 HC 1 LIG H3 3 -0.004 1.0080
so when i run minimization
( grompp -f em.mdp -p topol.top -c solvated.gro -o em.tpr )
Fatal error:
Syntax error - File topol.top, line 682
Last line read:
'[ molecules ]'
Invalid order for directive molecules
please help me to solved this error
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