Hi everyone,
I'm repeatedly encountering an issue while trying to run tutorial B5 using AmberTools24 on Ubuntu 24.04. The command I used is as follows:
parmchk2 -i cro.prepin -f prepi -o frcmod.cro -a Y -p $AMBERHOME/dat/leap/parm/parm10.dat
After executing this command, the process stops with the following message, resulting in an empty ‘frcmod.cro’ file and an ‘ANTECHAMBER.FRCMOD’ file sized 15.4 kb. I've attached the prepin file for reference.
Error Message:
*** buffer overflow detected ***: terminated
/Desktop/Amber/amber24/bin/parmchk2: line 9: 37737 Aborted (core dumped) "$AMBERHOME/bin/wrapped_progs/parmchk2" "$."
I'd appreciate any suggestions or insights into what might be causing this issue.
Thank you so much for your help!
Best regards,
Siqiong.
-------------------
cro.prepin
-----------------------------
0 0 2
This is a remark line
molecule.res
CRO INT 0
CORRECT OMIT DU BEG
0.0000
1 DUMM DU M 0 -1 -2 0.000 .0 .0 .00000
2 DUMM DU M 1 0 -1 1.449 .0 .0 .00000
3 DUMM DU M 2 1 0 1.523 111.21 .0 .00000
4 N1 N M 3 2 1 1.540 111.208 -180.000 -0.840430
5 CA1 CT M 4 3 2 1.470 51.789 -136.965 0.120197
6 CB1 CT 3 5 4 3 1.530 109.482 93.067 0.117967
7 CG1 CT 3 6 5 4 1.531 109.493 -54.989 -0.130502
8 HG11 HC E 7 6 5 1.090 109.454 59.932 0.055957
9 HG12 HC E 7 6 5 1.089 109.459 179.977 0.055957
10 HG13 HC E 7 6 5 1.090 109.422 -60.030 0.055957
11 OG1 OH S 6 5 4 1.429 109.459 65.002 -0.548653
12 HOG1 HO E 11 6 5 0.967 113.986 -60.029 0.415168
13 HB1 H1 E 6 5 4 1.090 109.525 -175.013 0.101615
14 HA1 H1 E 5 4 3 1.090 109.482 -26.917 0.096306
15 C1 CK M 5 4 3 1.507 109.461 -146.922 0.490451
16 N2 NB S 15 5 4 1.296 124.314 -34.708 -0.535987
17 CA2 CC B 16 15 5 1.368 109.276 179.990 -0.024018
18 C2 C S 17 16 15 1.473 105.758 -0.119 0.722775
19 O2 O E 18 17 16 1.218 127.388 -179.882 -0.546495
20 CB2 CD B 17 16 15 1.378 127.066 179.936 0.035889
21 CG2 CA S 20 17 16 1.464 120.040 -5.080 -0.117086
22 CD1 CA B 21 20 17 1.402 120.134 6.269 -0.050193
23 CE1 CA B 22 21 20 1.371 119.834 179.745 -0.187169
24 CZ CA B 23 22 21 1.391 120.184 -0.048 0.156192
25 CE2 CA B 24 23 22 1.391 120.259 0.344 -0.187169
26 CD2 CA S 25 24 23 1.372 120.097 -0.620 -0.050193
27 HD2 HA E 26 25 24 1.080 120.047 -179.414 0.161926
28 HE2 HA E 25 24 23 1.080 119.952 179.982 0.155555
29 OH OH S 24 23 22 1.357 119.901 -179.992 -0.462621
30 HOH HO E 29 24 23 0.967 114.009 89.978 0.449146
31 HE1 HA E 23 22 21 1.080 119.940 -179.692 0.155555
32 HD1 HA E 22 21 20 1.080 120.031 -0.292 0.161926
33 HB2 HA E 20 17 16 1.080 119.931 174.833 0.156086
34 N3 N* M 15 5 4 1.367 124.328 145.023 -0.409332
35 CA3 CT M 34 15 5 1.465 125.821 -0.020 0.074327
36 HA31 H1 E 35 34 15 1.090 109.428 -149.970 0.109579
37 HA32 H1 E 35 34 15 1.090 109.472 -30.034 0.109579
38 C3 C M 35 34 15 1.507 109.460 90.009 0.655244
39 O3 O E 38 35 34 1.208 120.048 -0.038 -0.523509
LOOP
N3 C2
CD2 CG2
IMPROPER
CA1 N3 C1 N2
C2 CB2 CA2 N2
CA2 N3 C2 O2
CG2 CA2 CB2 HB2
CD1 CD2 CG2 CB2
CG2 CE1 CD1 HD1
CD1 CZ CE1 HE1
CE1 CE2 CZ OH
CZ CD2 CE2 HE2
CG2 CE2 CD2 HD2
C2 C1 N3 CA3
CA3 +M C3 O3
DONE
STOP
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Received on Mon Dec 09 2024 - 02:00:02 PST
