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