GMX_order - Fatal error: grp 1 does not have same number of elements as grp 1

User discussions
1

GROMACS version: 2022
GROMACS modification: No

I am trying to run deuterium order parameter analysis on SAPE lipids of a heterogenous membrane. I made the index file for the first acyl chain using the following:

gmx_mpi make_ndx -f prot_eql.gro -o index_sape.ndx

First Prompt Selection:
r SAPE & a C36| r SAPE & a C37| r SAPE & a C38| r SAPE & a C39| r SAPE & a C40| r SAPE & a C41| r SAPE & a C42| r SAPE & a C43| r SAPE & a C44| r SAPE & a C45| r SAPE & a C46| r SAPE & a C47| r SAPE & a C48| r SAPE & a C49| r SAPE & a C50| r SAPE & a C51| r SAPE & a C52| r SAPE & a C53| r SAPE & a C54| r SAPE & a C55| r SAPE & a C56| r SAPE & a C57| r SAPE & a C58| r SAPE & a C59| r SAPE & a C60| r SAPE & a C61| r SAPE & a C62| r SAPE & a C63| r SAPE & a C64| r SAPE & a C65| r SAPE & a C66| r SAPE & a C67| r SAPE & a C68| r SAPE & a C69| r SAPE & a C70| r SAPE & a C71| r SAPE & a C72| r SAPE & a C73| r SAPE & a C74| r SAPE & a C75| r SAPE & a C76| r SAPE & a C77| r SAPE & a C78| r SAPE & a C79| r SAPE & a C80| r SAPE & a C81| r SAPE & a C82

I then try to run the command and select the chain1 group using:
gmx order -s md.tpr -f md.xtc -n index_sape.ndx -d z -od SAPE_chain1.xvg

The error I receive is:
Fatal error: grp 1 does not have same number of elements as grp 1

Can anyone verify if this is an indexing issue. If it is then what is the appropriate way to set up the index for gmx order?

2

The index group is incorrect. There should be separate groups for C36, C37, etc.

See http://www.mdtutorials.com/gmx/membrane_protein/09_analysis.html

3

I made the index file with the following script. I tried both with and without renaming each index group for acyl chain carbons to see if it made a difference and it did not. I still receive the same error when running echo 25 | gmx_mpi order -s md.tpr -f md.xtc -n index_sape.ndx -d z -od sape_ch1.xvg:

gmx_mpi make_ndx -f prot_eql.gro -o index_SAPE_dop.ndx <<EOF

r SAPE & a C23
name 25 C23
r SAPE & a C24
name 26 C24
r SAPE & a C25
name 27 C25
r SAPE & a C26
name 28 C26
r SAPE & a C27
name 29 C27
r SAPE & a C28
name 30 C28
r SAPE & a C29
name 31 C29
r SAPE & a C210
name 32 C30
r SAPE & a C211
name 33 C31
r SAPE & a C212
name 34 C32
r SAPE & a C213
name 35 C33
r SAPE & a C214
name 36 C34
r SAPE & a C215
name 37 C35
r SAPE & a C216
name 38 C36
r SAPE & a C217
name 39 C37
r SAPE & a C218
name 40 C38
r SAPE & a C219
name 41 C39
r SAPE & a C220
name 42 C40
r SAPE & a C33
name 43 C41
r SAPE & a C34
name 44 C42
r SAPE & a C35
name 45 C43
r SAPE & a C36
name 46 C44
r SAPE & a C37
name 47 C45
r SAPE & a C38
name 48 C46
r SAPE & a C39
name 49 C47
r SAPE & a C310
name 50 C48
r SAPE & a C311
name 51 C49
r SAPE & a C312
name 52 C50
r SAPE & a C313
name 53 C51
r SAPE & a C314
name 54 C52
r SAPE & a C315
name 55 C53
r SAPE & a C316
name 56 C54
r SAPE & a C317
name 57 C55
r SAPE & a C318
name 58 C56
r SAPE & a C319
name 59 C57
r SAPE & a C320
name 60 C58

q

EOF

4

What does gmx check tell you about the index file?

5

image
image1717×717 132 KB

Code:
gmx_mpi check -n index_SAPE_dop.ndx

Contents of index file index_SAPE_dop.ndx

Nr. Group #Entries First Last
0 System 632834 1 632834
1 Protein 4017 1 4017
2 Protein-H 2019 1 4017
3 C-alpha 251 5 4008
4 Backbone 753 1 4015
5 MainChain 1003 1 4015
6 MainChain+Cb 1239 1 4015
7 MainChain+H 1234 1 4015
8 SideChain 2783 2 4017
9 SideChain-H 1016 7 4017
10 Prot-Masses 4017 1 4017
11 non-Protein 628817 4018 632834
12 Other 628817 4018 632834
13 POPE 4000 4018 8017
14 PLPC 13464 8018 21481
15 PLPE 6888 21482 28369
16 SAPE 22008 28370 50377
17 TLCL1 31571 50378 81948
18 SAPC 23660 81949 105608
19 SAPS 2926 105609 108534
20 POPC 4824 108535 113358
21 SAPI 5577 113359 118935
22 SOD 515 118936 119450
23 CLA 315 119451 119765
24 TIP3 513069 119766 632834
25 C23 168 28405 50282
26 C24 168 28408 50285
27 C25 168 28411 50288
28 C26 168 28413 50290
29 C27 168 28415 50292
30 C28 168 28418 50295
31 C29 168 28420 50297
32 C30 168 28422 50299
33 C31 168 28425 50302
34 C32 168 28427 50304
35 C33 168 28429 50306
36 C34 168 28432 50309
37 C35 168 28434 50311
38 C36 168 28436 50313
39 C37 168 28439 50316
40 C38 168 28442 50319
41 C39 168 28445 50322
42 C40 168 28448 50325
43 C41 168 28452 50329
44 C42 168 28455 50332
45 C43 168 28458 50335
46 C44 168 28461 50338
47 C45 168 28464 50341
48 C46 168 28467 50344
49 C47 168 28470 50347
50 C48 168 28473 50350
51 C49 168 28476 50353
52 C50 168 28479 50356
53 C51 168 28482 50359
54 C52 168 28485 50362
55 C53 168 28488 50365
56 C54 168 28491 50368
57 C55 168 28494 50371
58 C56 168 28497 50374
59 C57 22008 28370 50377
60 C58 22008 28370 50377

6

You need to delete the unnecessary groups as noted in the tutorial link. Anything that isn’t an actor chain carbon needs to go. And your last two groups have a problem because they have far more atoms than all the others so you need to check how you created them.