Dear Experts,
This is regarding incorporating multiple restraints in my amber dist.RST
file.
I found a few links in dealing with these circumstances (
http://archive.ambermd.org/201801/0233.html,
https://www.researchgate.net/post/How_to_carry_MD_simulations_with_distance_constraint_between_two_residues
, Re: [AMBER] How can I run PMEMD with multiple distance restraints? from
David A Case on 2018-04-12 (Amber Archive Apr 2018) (ambermd.org)
<
http://archive.ambermd.org/201804/0109.html>,
http://ambermd.org/tutorials/advanced/tutorial4/index.htm).
But I could not find a specific solution to my problem.
I already have center-of-mass-distance restraints between two pairs of atom
clusters, corresponding to C-alpha atoms of two monomers, in a dimeric
system.
Apart from that, I want to incorporate an elastic network model kind of
restraint between the C-alpha carbons, which are at least 5 residues apart
from each other.
For checking my input file, I first incorporated one of the separation
between two selected Alpha carbons, along with the previously existing
c.o.m.d. distance between the two monomers.
The distRST input file is as follows:
# Change distance between C-ter of PROE and helix-3 of PROB from 9.6 A to
100.0 A
&rst
iat = -1, -1,
r1 = 1, r2 = 27.5, r3 = 28.0, r4 = 100,
rk2 = 10.0, rk3 = 10.0,
igr1 = 5, 24, 43, 53, 70, 82, 99, 118, 128, 145, 165, 176, 183, 207, 226,
240, 257, 274, 291, 305, 321, 338, 352, 359, 381, 405, 417, 428, 442, 454,
465, 472, 486, 508, 522, 533, 552, 564, 578, 600, 615, 622, 641, 660, 677,
698, 709, 726, 741, 757, 780, 792, 807, 826, 843, 862, 876, 890, 906, 922,
937, 947, 961, 980, 992, 1008, 1022, 1041, 1058, 1072, 1096, 1107, 1129,
1153, 1160, 1184, 1206, 1223, 1234, 1256, 1270, 1289, 1301, 1318, 1338,
1354, 1375, 1387, 1408, 1432, 1443, 1462, 1478, 1485, 1500, 1520, 1536,
1547, 1559, 1569, 1588, 1607, 1625, 1637, 1649, 1671, 1682, 1704, 1724,
1743, 1760, 1777, 1792, 1816, 1833, 1845, 1861, 1872, 1887, 1901, 1918,
1937, 1954, 1978, 1995, 2009, 2025, 2035, 2057, 2072, 2086, 2097, 2108,
2123, 2145, 2156, 2170, 2184, 2203, 2220, 2232, 2253, 2260, 2277, 2296,
2317, 2329, 2340, 2347, 2366, 2378, 2400, 2420, 2444, 2451, 2467, 2482,
2502, 2518, 2529, 2542, 2554,
igr2 = 2576, 2586, 2602, 2614, 2636, 2657, 2676, 2691, 2707, 2719, 2726,
2738, 2753, 2767, 2782, 2799, 2809, 2826, 2846, 2863, 2885, 2895, 2917,
2932, 2956, 2975, 2990, 3000, 3022, 3039, 3063, 3078, 3102, 3119, 3130,
3147, 3163, 3180, 3204, 3219, 3243, 3258, 3273, 3283, 3298, 3322, 3339,
3349, 3371, 3385, 3406, 3418, 3440, 3450, 3462, 3484, 3506, 3516, 3532,
3551, 3568, 3585, 3605, 3622, 3637, 3659, 3675, 3690, 3701, 3720, 3735,
3752, 3767, 3777, 3787, 3801, 3816, 3840, 3857, 3874, 3893, 3909, 3924,
3938, 3955, 3972, 3982, 4006, 4022, 4037, 4047, 4064, 4083, 4097, 4109,
4133, 4157, 4181, 4200, 4210, 4229, 4244, 4258, 4279, 4298, 4312, 4322,
4341, 4358, 4368, 4386, 4400, 4412, 4438, 4450, 4474, 4491, 4507, 4527,
4541, 4558, 4577, 4599, 4621, 4642, 4658, 4682, 4692, 4707, 4724, 4746,
4758, 4782, 4799, 4816, 4830, 4849, 4871, 4888, 4908, 4923, 4940, 4956,
4980, 4997, 5013, 5027, 5039, 5061, 5083, 5093, 5103, 5120, 5139, 5163,
5174, 5191, 5207, 5224, 5238, 5255, 5274, 5298, 5314, 5333, 5354, 5369,
5393, 5410, 5424, 5441, 5452, 5471, 5482, 5501, 5520, 5541, 5555, 5573,
5585, 5595, 5611, 5621, 5636, 5651, 5670, 5687, 5699, 5714, 5730, 5742,
5757,
nstep1 = 0, nstep2 = 0,
/
&end
#
## 1 GUA H1' 1 GUA H3' 4.6
&rst
ixpk = 0, nxpk = 0, iat = 70, 145, r1= 1.30, r2 = 1.80, r3 = 4.60, r4 =
5.10,
rk2 = 0.0, rk3 = 0.0, ir6 = 1, ialtd = 0,
/
&end
Without the latter part (between the two "&end" as specified above), the
simulation was running fine.
But with the specified additional inclusion, the job is failing with the
following error message:
At line 1052 of file
/home/juyong/apps/amber20_src/src/pmemd/src/nmr_calls.F90 (unit = 33, file
= 'dist1.RST')
Fortran runtime error: Cannot match namelist object name #
Request you to kindly help me sort out the problem.
Thank you in anticipation and inconvenience deeply regretted.
Sincerely,
Prathit Chatterjee
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Received on Tue Mar 01 2022 - 19:00:02 PST
