[gmx-users] Fwd: atoms are not part of any of the T-Coupling groups

Tue May 7 07:41:28 CEST 2019

---------- Forwarded message ---------
From: ISHRAT JAHAN <jishrat17 at gmail.com>
Date: Tue, May 7, 2019 at 11:05 AM
Subject: atoms are not part of any of the T-Coupling groups
To: <gromacs.org_gmx-users at maillist.sys.kth.se>

Dear all,
I am trying to calculate the lennard Jones interaction energy between
protein and urea in the first solvation shell. I have made the index group
of urea molecule in the first solvation shell and then tried to generate
the .tpr file using that index. After running the command
gmx grompp -f full.mdp -p ../prot.top -c ../prot_u3M_200ns.tpr -o
prot_u3M_rerun -n water_urea_5ofprot.ndx
following error occur-
35099 atoms are not part of any of the T-Coupling groups
part of  .mdp file and index file is given below
rvdw                =  1.2^M
fourierspacing = 0.12^M
fourier_nx = 0^M
fourier_ny = 0^M
fourier_nz = 0^M
pme_order = 4^M
ewald_rtol = 1e-5^M
optimize_fft = yes^M
; Berendsen temperature coupling is on in two groups^M
Tcoupl              =  V-rescale^M
tc-grps             =  Protein   Urea_5ofprot^M
tau_t               =  0.1        0.1             ^M
ref_t               =  300        300       ^M
; Energy monitoring^M
energygrps          =  Protein  Urea_5ofprot
; Isotropic pressure coupling is now on^M
Pcoupl              =  berendsen^M
 and at the end of the Index file i have only added the residue index of
urea within 5 of protein and save the index file.

[ Urea_5ofprot ]
1261 1262 1263 1264 1265 1266 1267 1268 1301 1302 1303 1304 1305 1306 1307
1308 1349 1350 1351 1352 1353 1354 1355 1356 1357 1358 1359 1360 1361 1362
1363 1364 1413 1414 1415 1416 1417 1418 1419 1420 1501 1502 1503 1504 1505
1506 1507 1508 1517 1518 1519 1520 1521 1522 1523 1524 1581 1582 1583 1584
1585 1586 1587 1588 1637 1638 1639 1640 1641 1642 1643 1644 1685 1686 1687
1688 1689 1690 1691 1692 1725 1726 1727 1728 1729 1730 1731 1732 1741 1742
1743 1744 1745 1746 1747 1748 1773 1774 1775 1776 1777 1778 1779 1780 1781
1782 1783 1784 1785 1786 1787 1788 1797 1798 1799 1800 1801 1802 1803 1804
1893 1894 1895 1896 1897 1898 1899 1900 1933 1934 1935 1936 1937 1938 1939
1940 1989 1990 1991 1992 1993 1994 1995 1996 2021 2022 2023 2024 2025 2026
2027 2028 2253 2254 2255 2256 2257 2258 2259 2260 2269 2270 2271 2272 2273
2274 2275 2276 2285 2286 2287 2288 2289 2290 2291 2292 2333 2334 2335 2336
2337 2338 2339 2340 2341 2342 2343 2344 2345 2346 2347 2348 2365 2366 2367
2368 2369 2370 2371 2372 2493 2494 2495 2496 2497 2498 2499 2500 2501 2502
2503 2504 2505 2506 2507 2508 2533 2534 2535 2536 2537 2538 2539 2540 2557
2558 2559 2560 2561 2562 2563 2564 2621 2622 2623 2624 2625 2626 2627 2628
2765 2766 2767 2768 2769 2770 2771 2772 2797 2798 2799 2800 2801 2802 2803
2804 2901 2902 2903 2904 2905 2906 2907 2908 2917 2918 2919 2920 2921 2922
2923 2924 2949 2950 2951 2952 2953 2954 2955 2956 3125 3126 3127 3128 3129
3130 3131 3132 3237 3238 3239 3240 3241 3242 3243 3244 3325 3326 3327 3328
3329 3330 3331 3332 3373 3374 3375 3376 3377 3378 3379 3380 3421 3422 3423
3424 3425 3426 3427 3428 3477 3478 3479 3480 3481 3482 3483 3484 3541 3542
3543 3544 3545 3546 3547 3548 3677 3678 3679 3680 3681 3682 3683 3684 3941
3942 3943 3944 3945 3946 3947 3948 3949 3950 3951 3952 3953 3954 3955 3956
3973 3974 3975 3976 3977 3978 3979 3980 4117 4118 4119 4120 4121 4122 4123
4124 4189 4190 4191 4192 4193 4194 4195 4196 4205 4206 4207 4208 4209 4210
4211 4212 4245 4246 4247 4248 4249 4250 4251 4252 4333 4334 4335 4336 4337
4338 4339 4340 4381 4382 4383 4384 4385 4386 4387 4388 4637 4638 4639 4640
4641 4642 4643 4644 4669 4670 4671 4672 4673 4674 4675 4676 4701 4702 4703
4704 4705 4706 4707 4708 4733 4734 4735 4736 4737 4738 4739 4740 4781 4782
4783 4784 4785 4786 4787 4788 4861 4862 4863 4864 4865 4866 4867 4868 4893
4894 4895 4896 4897 4898 4899 4900 4933 4934 4935 4936 4937 4938 4939 4940
5021 5022 5023 5024 5025 5026 5027 5028 5085 5086 5087 5088 5089 5090 5091
5092 5117 5118 5119 5120 5121 5122 5123 5124 5189 5190 5191 5192 5193 5194
5195 5196 5245 5246 5247 5248 5249 5250 5251 5252 5253 5254 5255 5256 5257
5258 5259 5260 5309 5310 5311 5312 5313 5314 5315 5316 5349 5350 5351 5352
5353 5354 5355 5356 5373 5374 5375 5376 5377 5378 5379 5380 5453 5454 5455
5456 5457 5458 5459 5460 5549 5550 5551 5552 5553 5554 5555 5556 5565 5566
5567 5568 5569 5570 5571 5572 5581 5582 5583 5584 5585 5586 5587 5588 5669
5670 5671 5672 5673 5674 5675 5676 5693 5694 5695 5696 5697 5698 5699 5700
5813 5814 5815 5816 5817 5818 5819 5820 5901 5902 5903 5904 5905 5906 5907
5908 5949 5950 5951 5952 5953 5954 5955 5956 5973 5974 5975 5976 5977 5978
5979 5980 6005 6006 6007 6008 6009 6010 6011 6012 6061 6062 6063 6064 6065
6066 6067 6068 6253 6254 6255 6256 6257 6258 6259 6260 6301 6302 6303 6304
6305 6306 6307 6308 6333 6334 6335 6336 6337 6338 6339 6340 6373 6374 6375
6376 6377 6378 6379 6380 6389 6390 6391 6392 6393 6394 6395 6396 6413 6414
6415 6416 6417 6418 6419 6420 6485 6486 6487 6488 6489 6490 6491 6492 6517
6518 6519 6520 6521 6522 6523 6524 6549 6550 6551 6552 6553 6554 6555 6556
6573 6574 6575 6576 6577 6578 6579 6580 6629 6630 6631 6632 6633 6634 6635
6636 6717 6718 6719 6720 6721 6722 6723 6724 6741 6742 6743 6744 6745 6746
6747 6748

-- 
Ishrat Jahan
Research Scholar
Department Of Chemistry
A.M.U Aligarh