[gmx-users] gmx_topolbuild error (aayattimg at bose.res.in)
Ray, Bruce D
bray at iupui.edu
Fri Jan 17 19:38:45 CET 2020
On Fri, 10 Jan 2020 11:15:36 +0530 (IST) , aayattimg at bose.res.in<mailto:aayattimg at bose.res.in> wrote:
Date: Fri, 10 Jan 2020 11:15:36 +0530 (IST)
From: aayattimg at bose.res.in<mailto:aayattimg at bose.res.in>
To: gromacs.org_gmx-users at maillist.sys.kth.se<mailto:gromacs.org_gmx-users at maillist.sys.kth.se>
Subject: [gmx-users] gmx_topolbuild error
Message-ID: <48026.103.230.166.2.1578635136.squirrel at bose.res.in><mailto:48026.103.230.166.2.1578635136.squirrel at bose.res.in>
Content-Type: text/plain;charset=UTF-8
I am getting error in topolbuild:
Fatal error.
Source code file: readmol2.c, line: 693
Atom 1 (O5') has 2 connections when allowed 0
I have used the command
./topolbuild -dir /home/aayatti/topolbuild1_2_1/dat/leap/parm -ff amber -n
tripos97
.mol2 file that I am using is as follows:
@<TRIPOS>MOLECULE
QCH
30 31 1 0 1
SMALL
USER_CHARGES
@<TRIPOS>ATOM
1 O5' -1.938234 2.221639 0.669368 O 1 QCH
-0.6458 ****
2 H5T -2.161090 3.085515 0.989879 H 1 QCH
0.4497 ****
3 O3' -3.459429 -1.728789 0.016186 O 1 QCH
-0.6852 ****
4 H3T -3.700920 -2.323917 0.713748 H 1 QCH
0.4392 ****
5 C1' -0.662286 -0.787261 -0.296578 C 1 QCH
0.3964 ****
6 H1' -0.605691 -1.741658 -0.791073 H 1 QCH
0.0394 ****
7 C2' -1.435951 -0.850884 1.016075 C 1 QCH
-0.0947 ****
8 H2'1 -1.108767 -0.064159 1.683744 H 1 QCH
0.0480 ****
9 H2'2 -1.331556 -1.807305 1.511592 H 1 QCH
0.0480 ****
10 C3' -2.859368 -0.575997 0.536996 C 1 QCH
0.2991 ****
11 H3' -3.474441 -0.127033 1.307751 H 1 QCH
0.0153 ****
12 C4' -2.644620 0.372686 -0.650794 C 1 QCH
0.1743 ****
13 H4' -3.310149 0.087545 -1.452894 H 1 QCH
0.0890 ****
14 C5' -2.828924 1.845500 -0.355885 C 1 QCH
0.0150 ****
15 H5'1 -2.633260 2.416008 -1.257986 H 1 QCH
0.0776 ****
16 H5'2 -3.858755 2.018514 -0.059368 H 1 QCH
0.0776 ****
17 O4' -1.304632 0.148647 -1.085285 O 1 QCH
-0.4154 ****
18 N1 0.746765 -0.330172 -0.139522 N 1 QCH
-0.0020 ****
19 C6 1.037481 0.982281 -0.067547 C 1 QCH
-0.1180 ****
20 H6 0.189023 1.636860 -0.090671 H 1 QCH
0.2766 ****
21 C5 2.303418 1.459166 0.033557 C 1 QCH
-0.2943 ****
22 H5 2.501789 2.509565 0.085307 H 1 QCH
0.1984 ****
23 C4 3.355190 0.521532 0.053970 C 1 QCH
0.4864 ****
24 N4 4.624825 0.860634 0.131082 N 1 QCH
-0.8725 ****
25 H41 5.362632 0.189871 0.139293 H 1 QCH
0.4651 ****
26 H42 4.887551 1.821377 0.170549 H 1 QCH
0.4651 ****
27 N3 3.028239 -0.778715 -0.004253 N 1 QCH
-0.2232 ****
28 H3 3.730821 -1.491229 0.018101 H 1 QCH
0.3215 ****
29 C2 1.731998 -1.290150 -0.085103 C 1 QCH
0.4517 ****
30 O2 1.543842 -2.458176 -0.098679 O 1 QCH
-0.4823 ****
@<TRIPOS>BOND
1 1 2 1
2 1 14 1
3 3 4 1
4 3 10 1
5 5 6 1
6 5 7 1
7 5 17 1
8 5 18 1
9 7 8 1
10 7 9 1
11 7 10 1
12 10 11 1
13 10 12 1
14 12 13 1
15 12 14 1
16 12 17 1
17 14 15 1
18 14 16 1
19 18 19 1
20 18 29 1
21 19 20 1
22 19 21 1
23 21 22 1
24 21 23 1
25 23 24 1
26 23 27 1
27 24 25 1
28 24 26 1
29 27 28 1
30 27 29 1
31 29 30 1
@<TRIPOS>SUBSTRUCTURE
1 QCH 1 **** 0 **** ****
kindly suggest to debug the error.
Thanking you in advance.
You do not have a properly formatted *.mol2 file. It lacks proper
Tripos atom types in the sixth column. In topolbuild, correct Tripos
atom types are critical for assignment of atom types in the final
gromacs topology. I am surprised that this error message was triggered
rather than a message about not being able to find the atom types. When
I get time now that I have been forced into retirement in my old age, I
hope to get back to refining this program, always provided that I am
able to remember what I did almost a decade ago. In the meantime,
your oxygens and carbons need proper Tripos atom topology types.
--
Bruce David Ray
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