[gmx-users] about porse.itp
Bhawana Gupta
bhawana.gupta2010 at gmail.com
Fri Nov 7 12:31:18 CET 2008
Dear gmx-users,
i made earlier asked this question .but there is a problem.
first i got the error:
-------------------------------------------------------
Program grompp, VERSION 4.0
Source code file: futil.c, line: 527
Fatal error:
Library file posre.itp not found in current dir nor in default directories.
(You can set the directories to search with the GMXLIB path variable)
Then on your advice, i put posre.itp in my directory, but i again got an
error.
-------------------------------------------------------
Program grompp, VERSION 4.0
Source code file: toppush.c, line: 1196
Fatal error:
[ file posre.itp, line 9 ]:
Atom index (5) in position_restraints out of bounds (1-3).
This probably means that you have inserted topology section
"position_restraints"
in a part belonging to a different molecule than you intended to.
In that case move the "position_restraints" section to the right molecule.
-------------------------------------------------------
This is the porse file which i have included.
; In this topology include file, you will find position restraint
; entries for all the heavy atoms in your original pdb file.
; This means that all the protons which were added by pdb2gmx are
; not restrained.
[ position_restraints ]
; atom type fx fy fz
1 1 1000 1000 1000
3 1 1000 1000 1000
5 1 1000 1000 1000
6 1 1000 1000 1000
7 1 1000 1000 1000
8 1 1000 1000 1000
9 1 1000 1000 1000
10 1 1000 1000 1000
13 1 1000 1000 1000
14 1 1000 1000 1000
15 1 1000 1000 1000
17 1 1000 1000 1000
18 1 1000 1000 1000
19 1 1000 1000 1000
20 1 1000 1000 1000
21 1 1000 1000 1000
22 1 1000 1000 1000
26 1 1000 1000 1000
27 1 1000 1000 1000
28 1 1000 1000 1000
30 1 1000 1000 1000
31 1 1000 1000 1000
32 1 1000 1000 1000
33 1 1000 1000 1000
34 1 1000 1000 1000
35 1 1000 1000 1000
36 1 1000 1000 1000
37 1 1000 1000 1000
39 1 1000 1000 1000
40 1 1000 1000 1000
41 1 1000 1000 1000
42 1 1000 1000 1000
43 1 1000 1000 1000
44 1 1000 1000 1000
45 1 1000 1000 1000
47 1 1000 1000 1000
48 1 1000 1000 1000
49 1 1000 1000 1000
50 1 1000 1000 1000
52 1 1000 1000 1000
54 1 1000 1000 1000
56 1 1000 1000 1000
58 1 1000 1000 1000
60 1 1000 1000 1000
61 1 1000 1000 1000
62 1 1000 1000 1000
64 1 1000 1000 1000
65 1 1000 1000 1000
66 1 1000 1000 1000
67 1 1000 1000 1000
69 1 1000 1000 1000
71 1 1000 1000 1000
73 1 1000 1000 1000
75 1 1000 1000 1000
77 1 1000 1000 1000
78 1 1000 1000 1000
79 1 1000 1000 1000
81 1 1000 1000 1000
82 1 1000 1000 1000
83 1 1000 1000 1000
84 1 1000 1000 1000
85 1 1000 1000 1000
87 1 1000 1000 1000
88 1 1000 1000 1000
89 1 1000 1000 1000
90 1 1000 1000 1000
91 1 1000 1000 1000
92 1 1000 1000 1000
93 1 1000 1000 1000
94 1 1000 1000 1000
95 1 1000 1000 1000
97 1 1000 1000 1000
98 1 1000 1000 1000
99 1 1000 1000 1000
100 1 1000 1000 1000
101 1 1000 1000 1000
102 1 1000 1000 1000
103 1 1000 1000 1000
104 1 1000 1000 1000
106 1 1000 1000 1000
107 1 1000 1000 1000
108 1 1000 1000 1000
109 1 1000 1000 1000
110 1 1000 1000 1000
111 1 1000 1000 1000
112 1 1000 1000 1000
114 1 1000 1000 1000
115 1 1000 1000 1000
116 1 1000 1000 1000
117 1 1000 1000 1000
119 1 1000 1000 1000
120 1 1000 1000 1000
121 1 1000 1000 1000
123 1 1000 1000 1000
124 1 1000 1000 1000
125 1 1000 1000 1000
127 1 1000 1000 1000
128 1 1000 1000 1000
129 1 1000 1000 1000
130 1 1000 1000 1000
131 1 1000 1000 1000
134 1 1000 1000 1000
135 1 1000 1000 1000
136 1 1000 1000 1000
138 1 1000 1000 1000
139 1 1000 1000 1000
140 1 1000 1000 1000
then i again make a posre.itp file , which i like this
; In this topology include file, you will find position restraint
; entries for all the heavy atoms in your original pdb file.
[ position_restraints ]
; atom type fx fy fz
AFTER THAT I GOT NO ERROR.
TELL ME WHETHER I AM CORRECT AT THIS POINT.
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