[gmx-users] Fwd: hydrogen bonds
Justin Lemkul
jalemkul at vt.edu
Mon Nov 2 11:37:59 CET 2015
On 11/2/15 12:01 AM, James Lord wrote:
> Hi all,
>
> I am trying to figure out the number of hydrogen bonds between a protein
> and membrane and which residues from protein were involved in hydrogen
> bonding. I made an index file and selected the protein and membrane,
>
> g_hbond -f md.xtc -s md.tpr -n index.ndx -num hbond.xvg -hbn hbond.ndx
>
> the hbond.xvg is giving me the number of hydrogen bonds and as far as I
> understood from manual hbond.ndx is should give me the atoms involved but I
> am confused seeing the output of hbond.ndx. What are the three columns at
> the end (atom numbers involved in hydrogen bonding)? Any comments?
>
Three atoms are required to define a hydrogen bond - donor, H, acceptor.
-Justin
>
> [ hbonds_Protein-MEM ]
> 1 2 6407
> 1 2 7982
> 1 2 7988
> 161 162 4391
> 201 202 4391
> 201 202 4523
> 201 202 5153
> 201 202 5174
> 201 202 5676
> 201 202 5678
> 253 254 3137
> 266 267 3131
> 266 267 5903
> 275 276 3131
> 275 276 5903
> 279 280 3257
> 279 280 3258
> 279 280 3261
> 279 280 3263
> 279 280 5903
> 279 280 5909
> 279 280 8864
> 301 302 2375
> 310 311 3257
> 310 311 3258
> 310 311 3263
> 310 311 3284
> 316 317 3284
> 323 324 2375
> 323 324 2402
> 323 324 3257
> 323 324 3258
> 323 324 3261
> 323 324 3263
> 323 324 3282
> 323 324 3284
> 323 324 5909
> 323 324 6974
> 323 324 6975
> 323 324 6999
> 323 324 7001
> 323 324 8675
> 323 324 8676
> 323 324 8702
> 323 324 8864
> 323 324 8865
> 323 324 8868
> 323 324 8870
> 323 324 8889
> 323 324 8891
> 332 333 2402
> 332 333 8681
> 332 333 8702
> 332 333 8864
> 332 333 8865
> 332 333 8868
> 332 333 8870
> 332 333 8889
> 332 333 8891
> 336 337 2375
> 336 337 2402
> 364 365 2402
> 367 368 2400
> 367 368 2402
> 367 368 8702
> 370 371 2402
> 370 371 8702
> 606 607 8045
> 606 607 8681
> 606 607 8864
> 606 607 8865
> 606 607 8868
> 606 607 8870
> 606 607 8889
> 606 607 8891
> 630 631 8675
> 630 631 8681
> 630 631 8702
> 974 975 7043
> 987 988 6218
> 987 988 6219
> 987 988 6224
> 987 988 6245
> 1131 1132 1809
> 1131 1132 1833
> 1131 1132 3131
> 1131 1132 3132
> 1131 1132 3135
> 1131 1132 3137
> 1131 1132 3158
> 1131 1132 6407
> 1131 1132 6413
> 1226 1227 4418
> 1226 1227 4517
> 1226 1227 6218
> 1226 1227 6245
> 1238 1239 4418
> 1238 1239 4517
> 1248 1249 4517
> 1248 1249 6224
> 1265 1266 6219
> 1299 1300 4859
> 1339 1340 4859
> 1355 1356 3320
> 1355 1356 3509
> 1355 1356 3510
> 1355 1356 3513
> 1355 1356 3515
> 1355 1356 4017
> 1355 1356 4019
> 1355 1356 4040
> 1355 1356 4838
> 1355 1356 7799
> 1383 1384 2501
> 1383 1384 3137
> 1383 1384 3158
> 1383 1384 3515
> 1383 1384 3536
> 1383 1384 4019
> 1383 1384 7169
> 1383 1384 7799
> 1383 1384 7982
> 1389 1390 7982
> 1395 1396 4013
> 1411 1412 3132
> 1411 1412 4013
> 1411 1412 4019
> 1428 1429 1808
> 1428 1429 1835
> 1428 1429 3131
> 1428 1429 3132
> 1428 1429 3135
> 1428 1429 3137
> 1428 1429 3156
> 1428 1429 3158
> 1428 1429 5930
> 1441 1442 3257
> 1447 1448 3131
> 1447 1448 3132
> 1447 1448 4013
> 1447 1448 4017
> 1447 1448 4019
> 1447 1448 4859
> 1450 1451 3131
> 1450 1451 3132
> 1450 1451 3135
> 1450 1451 3137
> 1450 1451 4013
> 1450 1451 4014
> 1450 1451 4017
> 1450 1451 4019
> 1450 1451 4838
> 1450 1451 4859
> 1453 1454 3131
> 1453 1454 3132
> 1453 1454 3137
> 1453 1454 3156
> 1453 1454 4013
> 1453 1454 4014
> 1453 1454 4017
> 1453 1454 4019
> 1453 1454 4859
> 1467 1468 2375
> 1467 1468 2379
> 1467 1468 3257
> 1467 1468 3258
> 1467 1468 3284
> 1471 1472 2375
> 1471 1472 2379
> 1471 1472 3257
> 1471 1472 3282
> 1471 1472 3284
> 1498 1499 4518
> 1498 1499 4523
> 1498 1499 5090
> 1498 1499 6180
> 1498 1499 6182
> 1510 1511 6182
> 1514 1515 4523
> 1514 1515 5153
> 1514 1515 5174
> 1514 1515 6182
> 1514 1515 6281
> 1514 1515 6287
> 1526 1527 4523
> 1526 1527 5084
> 1526 1527 5085
> 1526 1527 5088
> 1526 1527 5090
> 1526 1527 5111
> 1526 1527 5147
> 1526 1527 5148
> 1526 1527 5151
> 1526 1527 5153
> 1526 1527 5172
> 1526 1527 5174
> 1526 1527 6156
> 1526 1527 6180
> 1526 1527 6182
> 1526 1527 6282
> 1526 1527 6285
> 1526 1527 6287
> 1526 1527 6306
> 1526 1527 6308
> 1531 1532 5147
> 1531 1532 5148
> 1531 1532 5153
> 1531 1532 5172
> 1531 1532 5174
> 1531 1532 5678
> 1550 1551 5147
> 1567 1568 4139
> 1567 1568 5084
> 1567 1568 5777
> 1567 1568 5778
> 1567 1568 5802
> 1567 1568 5804
> 1567 1568 8234
> 1567 1568 8238
> 1567 1568 8240
> 1567 1568 8259
> 1567 1568 8261
> 1567 1568 8675
> 1567 1568 8676
> 1567 1568 8679
> 1567 1568 8681
> 1567 1568 8700
> 1567 1568 8702
> 1591 1592 5111
>
>
> Cheers,
> James
>
--
==================================================
Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
==================================================
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