On 3/21/13 2:12 AM, 라지브간디 wrote:
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Dear Justin,
I have checked my index.ndx file and it doesnt have any atoms close to 37872
atoms. I am bit confused why its happening.
There is some colossal mismatch between your coordinates, topology, and/or index
file. I would recommend eliminating all the freezing and special groups and try
to get a vanilla system working, then add complexity with the groups you're
trying to freeze. There's something more fundamentally wrong here that you need
to be solving first.
-Justin
Contents of index file fz.ndx
--------------------------------------------------
Nr. Group #Entries First Last
0 System 2124 1 2124
1 Protein 1522 1 1522
2 Protein-H 1204 1 1522
3 C-alpha 151 5 1506
4 Backbone 453 1 1520
5 MainChain 605 1 1522
6 MainChain+Cb 746 1 1522
7 MainChain+H 754 1 1522
8 SideChain 768 6 1519
9 SideChain-H 599 6 1518
10 Prot-Masses 1522 1 1522
11 non-Protein 602 1523 2124
12 Other 59 1523 1581
13 SO4 10 1523 1532
14 HEM 47 1533 1579
15 CMO 2 1580 1581
16 Water 543 1582 2124
17 SOL 543 1582 2124
18 non-Water 1581 1 1581
19 g1 10 28 37
20 g2 12 74 85
21 g3 12 241 252
22 g4 17 289 305
23 g5 10 400 409
24 g6 17 423 439
25 g7 17 449 465
26 g8 17 466 482
27 g9 13 483 495
28 g10 9 508 516
29 g11 13 574 586
30 g12 9 620 628
31 g13 13 642 654
32 g14 12 655 666
33 g15 12 897 908
34 g16 13 944 956
35 g17 10 1091 1100
36 g18 9 1145 1153
37 g19 12 1154 1165
38 g20 8 1166 1173
39 g21 17 1174 1190
40 g22 9 1254 1262
41 g23 12 1269 1280
42 g24 13 1312 1324
43 g25 10 1340 1349
44 g26 17 1359 1375
45 g27 9 1415 1423
46 g28 18 1449 1466
47 g29 19 1504 1522
Usually the "Protein Non-Protein" approach covers everything. Apparently in
your case, something is wrong and you will have to figure out what has not
been accounted for. Try using gmxcheck on your index file to see if there
is a group (or groups) whose contents account for 37872 atoms.
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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