[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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