GROMACS version: 2021.4
GROMACS modification: No
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Hi all I am having issues generating a topology for long chain hydrocarbons: For two differently bonded equal hydrocarbons I get errors.
The GRO file looks as follows:
LIGPARGEN GENERATED GRO FILE
30
1UNK C00 1 0.100 0.100 0.000
1UNK C01 2 -0.046 0.100 0.000
1UNK C02 3 -0.120 0.100 0.108
1UNK C03 4 -0.198 0.100 0.200
1UNK C04 5 -0.279 0.100 0.289
1UNK C05 6 -0.367 0.100 0.384
1UNK C06 7 0.176 0.100 -0.107
1UNK C07 8 0.256 0.100 -0.198
1UNK C08 9 0.335 0.100 -0.289
1UNK C09 10 0.415 0.100 -0.380
1UNK C0A 11 0.495 0.100 -0.485
1UNK C0B 12 0.437 0.100 -0.620
1UNK C0C 13 0.310 0.100 -0.647
1UNK C0D 14 0.193 0.100 -0.673
1UNK C0E 15 0.076 0.100 -0.699
1UNK C0F 16 -0.051 0.100 -0.726
1UNK C0G 17 0.641 0.099 -0.471
1UNK C0H 18 0.709 0.099 -0.361
1UNK C0I 19 0.782 0.099 -0.266
1UNK C0J 20 0.860 0.099 -0.162
1UNK H0K 21 0.149 0.100 0.097
1UNK H0M 22 -0.096 0.100 -0.097
1UNK H0N 23 -0.471 0.073 0.365
1UNK H0O 24 -0.340 0.127 0.486
1UNK H0P 25 0.507 0.100 -0.703
1UNK H0Q 26 -0.124 0.112 -0.647
1UNK H0R 27 -0.085 0.089 -0.828
1UNK H0S 28 0.697 0.099 -0.564
1UNK H0T 29 0.891 0.193 -0.116
1UNK H0U 30 0.896 0.006 -0.120
10.0000 10.0000 10.0000
The associated error I get is as follows:
Command line:
gmx x2top -f 1,6pentyldecanerigid.gro -o top.top
Opening force field file /usr/share/gromacs/top/oplsaa.ff/atomname2type.n2t
There are 23 name to type translations in file oplsaa.ff
Generating bonds from distances…
Can not find forcefield for atom C02-3 with 2 bonds
Can not find forcefield for atom C03-4 with 2 bonds
Can not find forcefield for atom C04-5 with 2 bonds
Can not find forcefield for atom C05-6 with 3 bonds
Can not find forcefield for atom C06-7 with 2 bonds
Can not find forcefield for atom C07-8 with 2 bonds
Can not find forcefield for atom C08-9 with 2 bonds
Can not find forcefield for atom C09-10 with 2 bonds
Can not find forcefield for atom C0A-11 with 3 bonds
Can not find forcefield for atom C0C-13 with 2 bonds
Can not find forcefield for atom C0D-14 with 2 bonds
Can not find forcefield for atom C0E-15 with 2 bonds
Can not find forcefield for atom C0F-16 with 3 bonds
Can not find forcefield for atom C0H-18 with 2 bonds
Can not find forcefield for atom C0I-19 with 2 bonds
Can not find forcefield for atom C0J-20 with 3 bonds
Program: gmx x2top, version 2021.4-Ubuntu-2021.4-2
Source file: src/gromacs/gmxpreprocess/x2top.cpp (line 186)
Fatal error:
Could only find a forcefield type for 14 out of 30 atoms
Thank you for your help!
Daniel
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