[gmx-users] topolbuild (Fatal error. Source code file: readmol2.c, line: 162)
Bruce D. Ray
bray at iupui.edu
Mon Nov 17 19:18:26 CET 2014
On Mon, 17 Nov 2014, at 18:54:00 +0330, leila karami <karami.leila1 at gmail.com> wrote:
>Dear gromacs users
>
>I installed topolbuild version 1.3. I used following command line:
>
>./topolbuild -n khob -dir ../dat/gromacs/ -ff gmx53a6.dat -meas
>
>I encountered with following error:
>
>Fatal error.
>Source code file: readmol2.c, line: 162
>Atomic symbol O2 in atom type not found.
>
>How to resolve this problem?
>
>Any help will highly appreciated.
I have pasted youyr mol2 file from your second message below.
On Mon, 17 Nov 2014, at 18:56:00 +0330, leila karami <karami.leila1 at gmail.com> wrote:
>my mol2file is as follows:
>
> @<TRIPOS>MOLECULE
>C:\Users\scc\Desktop\22.pdb
> 30 31 0 0 0
>SMALL
>GASTEIGER
>
>@<TRIPOS>ATOM
> 1 O2 0.9991 0.0511 -0.0859 O2 1 C1 -0.2444
> 2 C2 2.2266 0.0511 -0.0859 Car 1 C1 0.3522
> 3 N3 2.8760 2.9655 -4.9849 Nar 1 C1 -0.1783
> 4 C4 2.2266 2.3904 -4.0182 Car 1 C1 0.1230
> 5 N4 0.8301 2.3904 -4.0182 Npl 1 C1 -0.3430
> 6 C5 2.8981 1.7958 -3.0187 Car 1 C1 -0.0056
> 7 C6 2.2266 1.2012 -2.0192 Car 1 C1 0.0152
> 8 N1 2.8760 0.6262 -1.0526 Nar 1 C1 -0.2700
> 9 C1* 4.3105 0.6262 -1.0526 C3 1 C1 0.1680
> 10 H1* 4.6672 1.1419 -1.9196 H 1 C1 0.0867
> 11 O4* 6.2372 -0.7744 -3.5532 O3 1 C1 -0.3456
> 12 C4* 4.8172 -0.7744 -3.5532 C3 1 C1 0.1126
> 13 H4* 4.4605 -1.2673 -4.4334 H 1 C1 0.0647
> 14 C3* 4.3105 -1.5070 -2.3216 C3 1 C1 0.1135
> 15 H3* 3.2405 -1.5070 -2.3216 H 1 C1 0.0647
> 16 O3* 4.7839 -2.8457 -2.3391 O3 1 C1 -0.3864
> 17 C2* 4.8172 -0.8068 -1.0713 C3 1 C1 0.1286
> 18 H2* 5.8872 -0.8068 -1.0713 H 1 C1 0.0665
> 19 O2* 4.3439 -1.4913 0.0793 O3 1 C1 -0.3847
> 20 C5* 4.3105 0.6586 -3.5345 C3 1 C1 0.0730
> 21 O5* 2.8905 0.6586 -3.5345 O3 1 C1 -0.3924
> 22 H41 0.3301 1.9477 -3.2739 H 1 C1 0.1437
> 23 H42 0.3301 2.8332 -4.7625 H 1 C1 0.1437
> 24 H5 3.9301 1.7958 -3.0187 H 1 C1 0.0666
> 25 H6 1.1946 1.2012 -2.0192 H 1 C1 0.0812
> 26 H3* 5.7839 -2.8457 -2.3391 HO 1 C1 0.2100
> 27 H2* 4.6772 -2.4340 0.0670 HO 1 C1 0.2101
> 28 H5*1 4.6672 1.1515 -2.6543 H 1 C1 0.0584
> 29 H5*2 4.6672 1.1743 -4.4015 H 1 C1 0.0584
> 30 H5* 2.5572 0.1979 -4.3571 HO 1 C1 0.2095
>@<TRIPOS>BOND
> 1 1 2 2
> 2 2 3 ar
> 3 2 8 ar
> 4 3 4 ar
> 5 4 5 1
> 6 4 6 ar
> 7 5 22 1
> 8 5 23 1
> 9 6 7 ar
> 10 6 24 1
> 11 7 8 ar
> 12 7 25 1
> 13 8 9 1
> 14 9 11 1
> 15 9 17 1
> 16 9 10 1
> 17 11 12 1
> 18 12 13 1
> 19 12 14 1
> 20 12 20 1
> 21 14 17 1
> 22 14 16 1
> 23 14 15 1
> 24 16 26 1
> 25 17 18 1
> 26 17 19 1
> 27 19 27 1
> 28 20 21 1
> 29 20 28 1
> 30 20 29 1
> 31 21 30 1
The first thing I notice about this mol2 file is that none of the atom types given in
the sixth column are valid Tripos Sybyl atom types. For example, for the first four
atoms, the valid Tripos Sybyl atom types would be O.2, C.ar, N.ar, C.ar, and N.pl
Notice the "." character that separates the element from the type modifier. The program
searches for that character to determine what the element is, what bonding to expect,
and how to convert this information to the correct atom type for the topology.
The second thing I notice is that the mol2 file is not properly terminated. After the
last bond record is given, you need a line that reads @<TRIPOS> In a complete
mol2 file, this is typically @<TRIPOS>SUBSTRUCTURE The program only looks for the
@<TRIPOS> portion to be sure that everything needed is read.
Third, it appears that this file was created on a Windows machine. You might need to
run dos2unix on it to get the correct line terminatiions.
--
Bruce D. Ray, Ph.D.
Associate Scientist
IUPUI
Physics Dept.
402 N. Blackford St., Rm. LD-061
Indianapolis, IN 46202-3273
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