# Newbox generation error

**URL:** <https://gromacs.bioexcel.eu/t/newbox-generation-error/11757>\
**Category:** User discussions\
**Tags:** mdrun\
**Created:** [March 16, 2025, 4:51pm UTC](https://gromacs.bioexcel.eu/t/newbox-generation-error/11757 "2025-03-16T16:51:02Z")\
**Posts on this page:** 2\
**Page:** 1

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**Author:** ![James](https://avatars.discourse-cdn.com/v4/letter/j/bc8723/32.png) [@James](https://gromacs.bioexcel.eu/u/James)\
**Post date:** [March 16, 2025, 4:51pm UTC](https://gromacs.bioexcel.eu/t/newbox-generation-error/11757/1 "2025-03-16T16:51:02Z")

</div>

After generating the complex.gro, I used the command “editconf -f complex.gro -o newbox.gro -bt cubic -d 1.0” to define the solvation box. However, no coordinates are generated in the box.gro file (see below).  
Gallium Rubidium Oxygen Manganese Argon Carbon Silicon  
2279  
7TYR N 1 -nan -nan -nan  
7TYR H1 2 -nan -nan -nan  
7TYR H2 3 -nan -nan -nan  
7TYR H3 4 -nan -nan -nan  
7TYR CA 5 -nan -nan -nan  
7TYR HA 6 -nan -nan -nan  
7TYR CB 7 -nan -nan -nan  
7TYR HB1 8 -nan -nan -nan  
7TYR HB2 9 -nan -nan -nan  
7TYR CG 10 -nan -nan -nan  
7TYR CD1 11 -nan -nan -nan  
7TYR HD1 12 -nan -nan -nan  
7TYR CE1 13 -nan -nan -nan  
7TYR HE1 14 -nan -nan -nan  
7TYR CZ 15 -nan -nan -nan  
7TYR OH 16 -nan -nan -nan  
7TYR HH 17 -nan -nan -nan  
7TYR CD2 18 -nan -nan -nan  
7TYR HD2 19 -nan -nan -nan  
7TYR CE2 20 -nan -nan -nan  
7TYR HE2 21 -nan -nan -nan  
7TYR C 22 -nan -nan -nan  
7TYR O 23 -nan -nan -nan  
8ASP N 24 -nan -nan -nan  
8ASP HN 25 -nan -nan -nan  
8ASP CA 26 -nan -nan -nan  
8ASP HA 27 -nan -nan -nan  
8ASP CB 28 -nan -nan -nan  
8ASP HB1 29 -nan -nan -nan  
8ASP HB2 30 -nan -nan -nan  
8ASP CG 31 -nan -nan -nan  
8ASP OD1 32 -nan -nan -nan  
8ASP OD2 33 -nan -nan -nan  
8ASP C 34 -nan -nan -nan  
8ASP O 35 -nan -nan -nan  
9ASN N 36 -nan -nan -nan  
9ASN HN 37 -nan -nan -nan  
9ASN CA 38 -nan -nan -nan  
9ASN HA 39 -nan -nan -nan  
9ASN CB 40 -nan -nan -nan  
9ASN HB1 41 -nan -nan -nan  
9ASN HB2 42 -nan -nan -nan  
9ASN CG 43 -nan -nan -nan  
9ASN OD1 44 -nan -nan -nan  
9ASN ND2 45 -nan -nan -nan  
9ASN HD21 46 -nan -nan -nan  
9ASN HD22 47 -nan -nan -nan  
9ASN C 48 -nan -nan -nan  
9ASN O 49 -nan -nan -nan  
10ARG N 50 -nan -nan -nan  
10ARG HN 51 -nan -nan -nan  
10ARG CA 52 -nan -nan -nan  
10ARG HA 53 -nan -nan -nan  
10ARG CB 54 -nan -nan -nan  
10ARG HB1 55 -nan -nan -nan  
10ARG HB2 56 -nan -nan -nan  
10ARG CG 57 -nan -nan -nan  
10ARG HG1 58 -nan -nan -nan  
10ARG HG2 59 -nan -nan -nan  
10ARG CD 60 -nan -nan -nan  
10ARG HD1 61 -nan -nan -nan  
10ARG HD2 62 -nan -nan -nan  
10ARG NE 63 -nan -nan -nan  
10ARG HE 64 -nan -nan -nan  
10ARG CZ 65 -nan -nan -nan  
10ARG NH1 66 -nan -nan -nan  
10ARG HH11 67 -nan -nan -nan  
10ARG HH12 68 -nan -nan -nan  
10ARG NH2 69 -nan -nan -nan  
10ARG HH21 70 -nan -nan -nan  
10ARG HH22 71 -nan -nan -nan  
10ARG C 72 -nan -nan -nan  
10ARG O 73 -nan -nan -nan  
11GLU N 74 -nan -nan -nan  
11GLU HN 75 -nan -nan -nan  
11GLU CA 76 -nan -nan -nan  
11GLU HA 77 -nan -nan -nan  
11GLU CB 78 -nan -nan -nan  
11GLU HB1 79 -nan -nan -nan  
11GLU HB2 80 -nan -nan -nan  
11GLU CG 81 -nan -nan -nan  
11GLU HG1 82 -nan -nan -nan  
11GLU HG2 83 -nan -nan -nan  
11GLU CD 84 -nan -nan -nan  
11GLU OE1 85 -nan -nan -nan  
11GLU OE2 86 -nan -nan -nan  
11GLU C 87 -nan -nan -nan  
11GLU O 88 -nan -nan -nan  
12ILE N 89 -nan -nan -nan  
12ILE HN 90 -nan -nan -nan  
12ILE CA 91 -nan -nan -nan  
12ILE HA 92 -nan -nan -nan  
12ILE CB 93 -nan -nan -nan  
12ILE HB 94 -nan -nan -nan  
12ILE CG2 95 -nan -nan -nan  
12ILE HG21 96 -nan -nan -nan  
12ILE HG22 97 -nan -nan -nan  
12ILE HG23 98 -nan -nan -nan  
12ILE CG1 99 -nan -nan -nan  
12ILE HG11 100 -nan -nan -nan  
12ILE HG12 101 -nan -nan -nan  
12ILE CD 102 -nan -nan -nan  
12ILE HD1 103 -nan -nan -nan  
12ILE HD2 104 -nan -nan -nan  
12ILE HD3 105 -nan -nan -nan  
12ILE C 106 -nan -nan -nan  
12ILE O 107 -nan -nan -nan  
13VAL N 108 -nan -nan -nan  
13VAL HN 109 -nan -nan -nan  
13VAL CA 110 -nan -nan -nan  
13VAL HA 111 -nan -nan -nan  
13VAL CB 112 -nan -nan -nan  
13VAL HB 113 -nan -nan -nan  
13VAL CG1 114 -nan -nan -nan  
13VAL HG11 115 -nan -nan -nan  
13VAL HG12 116 -nan -nan -nan  
13VAL HG13 117 -nan -nan -nan  
13VAL CG2 118 -nan -nan -nan  
13VAL HG21 119 -nan -nan -nan  
13VAL HG22 120 -nan -nan -nan  
13VAL HG23 121 -nan -nan -nan  
13VAL C 122 -nan -nan -nan  
13VAL O 123 -nan -nan -nan  
14MET N 124 -nan -nan -nan  
14MET HN 125 -nan -nan -nan  
14MET CA 126 -nan -nan -nan  
14MET HA 127 -nan -nan -nan  
14MET CB 128 -nan -nan -nan  
14MET HB1 129 -nan -nan -nan  
14MET HB2 130 -nan -nan -nan  
14MET CG 131 -nan -nan -nan  
14MET HG1 132 -nan -nan -nan  
14MET HG2 133 -nan -nan -nan  
14MET SD 134 -nan -nan -nan  
14MET CE 135 -nan -nan -nan  
14MET HE1 136 -nan -nan -nan  
14MET HE2 137 -nan -nan -nan  
14MET HE3 138 -nan -nan -nan  
14MET C 139 -nan -nan -nan  
14MET O 140 -nan -nan -nan  
15LYS N 141 -nan -nan -nan  
15LYS HN 142 -nan -nan -nan  
15LYS CA 143 -nan -nan -nan  
15LYS HA 144 -nan -nan -nan  
15LYS CB 145 -nan -nan -nan  
15LYS HB1 146 -nan -nan -nan  
15LYS HB2 147 -nan -nan -nan  
15LYS CG 148 -nan -nan -nan  
15LYS HG1 149 -nan -nan -nan  
15LYS HG2 150 -nan -nan -nan  
15LYS CD 151 -nan -nan -nan  
15LYS HD1 152 -nan -nan -nan  
15LYS HD2 153 -nan -nan -nan  
15LYS CE 154 -nan -nan -nan  
15LYS HE1 155 -nan -nan -nan  
15LYS HE2 156 -nan -nan -nan  
15LYS NZ 157 -nan -nan -nan  
15LYS HZ1 158 -nan -nan -nan  
15LYS HZ2 159 -nan -nan -nan  
15LYS HZ3 160 -nan -nan -nan  
15LYS C 161 -nan -nan -nan  
15LYS O 162 -nan -nan -nan  
16TYR N 163 -nan -nan -nan  
16TYR HN 164 -nan -nan -nan  
16TYR CA 165 -nan -nan -nan  
16TYR HA 166 -nan -nan -nan  
16TYR CB 167 -nan -nan -nan  
16TYR HB1 168 -nan -nan -nan  
16TYR HB2 169 -nan -nan -nan  
16TYR CG 170 -nan -nan -nan  
16TYR CD1 171 -nan -nan -nan  
16TYR HD1 172 -nan -nan -nan  
16TYR CE1 173 -nan -nan -nan  
16TYR HE1 174 -nan -nan -nan  
16TYR CZ 175 -nan -nan -nan  
16TYR OH 176 -nan -nan -nan  
16TYR HH 177 -nan -nan -nan  
16TYR CD2 178 -nan -nan -nan  
16TYR HD2 179 -nan -nan -nan  
16TYR CE2 180 -nan -nan -nan  
16TYR HE2 181 -nan -nan -nan  
16TYR C 182 -nan -nan -nan  
16TYR O 183 -nan -nan -nan  
17ILE N 184 -nan -nan -nan  
17ILE HN 185 -nan -nan -nan  
17ILE CA 186 -nan -nan -nan  
17ILE HA 187 -nan -nan -nan  
17ILE CB 188 -nan -nan -nan  
17ILE HB 189 -nan -nan -nan  
17ILE CG2 190 -nan -nan -nan  
17ILE HG21 191 -nan -nan -nan  
17ILE HG22 192 -nan -nan -nan  
17ILE HG23 193 -nan -nan -nan  
17ILE CG1 194 -nan -nan -nan  
17ILE HG11 195 -nan -nan -nan  
17ILE HG12 196 -nan -nan -nan  
17ILE CD 197 -nan -nan -nan  
17ILE HD1 198 -nan -nan -nan  
17ILE HD2 199 -nan -nan -nan  
17ILE HD3 200 -nan -nan -nan  
17ILE C 201 -nan -nan -nan  
17ILE O 202 -nan -nan -nan  
18HIS N 203 -nan -nan -nan  
18HIS HN 204 -nan -nan -nan  
18HIS CA 205 -nan -nan -nan  
18HIS HA 206 -nan -nan -nan  
18HIS CB 207 -nan -nan -nan  
18HIS HB1 208 -nan -nan -nan  
18HIS HB2 209 -nan -nan -nan  
18HIS ND1 210 -nan -nan -nan  
18HIS CG 211 -nan -nan -nan  
18HIS CE1 212 -nan -nan -nan  
18HIS HE1 213 -nan -nan -nan  
18HIS NE2 214 -nan -nan -nan  
18HIS HE2 215 -nan -nan -nan  
18HIS CD2 216 -nan -nan -nan  
18HIS HD2 217 -nan -nan -nan  
18HIS C 218 -nan -nan -nan  
18HIS O 219 -nan -nan -nan  
19TYR N 220 -nan -nan -nan  
19TYR HN 221 -nan -nan -nan  
(..)  
6.63523 6.63523 6.63523

What could be the reason for this error?

Thank you in advance!

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<div class="post-metadata">

**Author:** ![alevilla](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/alevilla/32/439_2.png) [@alevilla](https://gromacs.bioexcel.eu/u/alevilla)\
**Post date:** [March 24, 2025, 9:47am UTC](https://gromacs.bioexcel.eu/t/newbox-generation-error/11757/2 "2025-03-24T09:47:37Z")

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Hi,  
Which GROMACS version are you using?  
You could check how complex.gro looks like?  
\Alessandra