[gmx-users] gmx_topolbuild error
Alessandra Villa
alessandra.villa.biosim at gmail.com
Fri Jan 10 10:12:51 CET 2020
Hi,
I am not familiar with the software "topolbuild" (gmx topolbuild does not
exist), but I have noticed that you are not using TRIPOS atom types in
your mol2 file.
Maybe that is a problem.
Best regards
Alessandra
On Fri, Jan 10, 2020 at 7:03 AM <aayattimg at bose.res.in> wrote:
> 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.
>
> --
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