GROMACS version: 2020.5
GROMACS modification: Yes
Hi,
I am trying to run MD simulation for a protein-peptide complex having two sulfotyrosine residues using AMBER99sb-ILDN force field. I followed the gromacs tutorial “Adding a Residue to a Force Field” , and edited the .rtp and .hbd files and successfully generated the .gro and .itp and .top files for complex. But while adding ions, it is showing following error:
**~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~**
GROMACS: gmx grompp, version 2020.5
Executable: /usr/local/gromacs/bin/gmx_mpi
Data prefix: /usr/local/gromacs
Working dir: /media/kmlab/e0a76a38-d3f0-409e-8cf5-7d35c284604d/Nupur/sulfopeptide_Tyr3739
Command line:
** gmx_mpi grompp -f ions.mdp -c cxc3_B_em_solv.gro -p topol.top -o ions.tpr**
Ignoring obsolete mdp entry 'ns_type’
NOTE 1 [file ions.mdp]:
** With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note**
** that with the Verlet scheme, nstlist has no effect on the accuracy of**
** your simulation.**
Setting the LD random seed to -75558916
Generated 2145 of the 2145 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 0.5
Generated 2145 of the 2145 1-4 parameter combinations
ERROR 1 [file topol_Protein_chain_B.itp, line 333]:
** No default Bond types**
ERROR 2 [file topol_Protein_chain_B.itp, line 334]:
** No default Bond types**
ERROR 3 [file topol_Protein_chain_B.itp, line 335]:
** No default Bond types**
ERROR 4 [file topol_Protein_chain_B.itp, line 336]:
** No default Bond types**
ERROR 5 [file topol_Protein_chain_B.itp, line 370]:
** No default Bond types**
ERROR 6 [file topol_Protein_chain_B.itp, line 371]:
** No default Bond types**
ERROR 7 [file topol_Protein_chain_B.itp, line 372]:
** No default Bond types**
ERROR 8 [file topol_Protein_chain_B.itp, line 373]:
** No default Bond types**
ERROR 9 [file topol_Protein_chain_B.itp, line 1115]:
** No default Angle types**
ERROR 10 [file topol_Protein_chain_B.itp, line 1117]:
** No default Angle types**
ERROR 11 [file topol_Protein_chain_B.itp, line 1118]:
** No default Angle types**
ERROR 12 [file topol_Protein_chain_B.itp, line 1119]:
** No default Angle types**
ERROR 13 [file topol_Protein_chain_B.itp, line 1120]:
** No default Angle types**
ERROR 14 [file topol_Protein_chain_B.itp, line 1121]:
** No default Angle types**
ERROR 15 [file topol_Protein_chain_B.itp, line 1122]:
** No default Angle types**
ERROR 16 [file topol_Protein_chain_B.itp, line 1123]:
** No default Angle types**
ERROR 17 [file topol_Protein_chain_B.itp, line 1124]:
** No default Angle types**
ERROR 18 [file topol_Protein_chain_B.itp, line 1179]:
** No default Angle types**
ERROR 19 [file topol_Protein_chain_B.itp, line 1181]:
** No default Angle types**
ERROR 20 [file topol_Protein_chain_B.itp, line 1182]:
** No default Angle types**
ERROR 21 [file topol_Protein_chain_B.itp, line 1183]:
** No default Angle types**
ERROR 22 [file topol_Protein_chain_B.itp, line 1184]:
** No default Angle types**
ERROR 23 [file topol_Protein_chain_B.itp, line 1185]:
** No default Angle types**
ERROR 24 [file topol_Protein_chain_B.itp, line 1186]:
** No default Angle types**
ERROR 25 [file topol_Protein_chain_B.itp, line 1187]:
** No default Angle types**
ERROR 26 [file topol_Protein_chain_B.itp, line 1188]:
** No default Angle types**
ERROR 27 [file topol_Protein_chain_B.itp, line 1568]:
** No default Proper Dih. types**
ERROR 28 [file topol_Protein_chain_B.itp, line 1569]:
** No default Proper Dih. types**
ERROR 29 [file topol_Protein_chain_B.itp, line 1570]:
** No default Proper Dih. types**
ERROR 30 [file topol_Protein_chain_B.itp, line 1674]:
** No default Proper Dih. types**
ERROR 31 [file topol_Protein_chain_B.itp, line 1675]:
** No default Proper Dih. types**
ERROR 32 [file topol_Protein_chain_B.itp, line 1676]:
** No default Proper Dih. types**
ERROR 33 [file topol_Protein_chain_B.itp, line 1899]:
** No default Improper Dih. types**
ERROR 34 [file topol_Protein_chain_B.itp, line 1901]:
** No default Improper Dih. types**
ERROR 35 [file topol_Protein_chain_B.itp, line 1911]:
** No default Improper Dih. types**
ERROR 36 [file topol_Protein_chain_B.itp, line 1913]:
** No default Improper Dih. types**
Excluding 3 bonded neighbours molecule type 'Protein_chain_A’
Excluding 3 bonded neighbours molecule type 'Protein_chain_B’
Excluding 2 bonded neighbours molecule type 'SOL’
NOTE 2 [file topol.top, line 48]:
** System has non-zero total charge: -1.000000**
** Total charge should normally be an integer. See**
** http://www.gromacs.org/Documentation/Floating_Point_Arithmetic**
** for discussion on how close it should be to an integer.**
There were 2 notes
-------------------------------------------------------
Program: gmx grompp, version 2020.5
Source file: src/gromacs/gmxpreprocess/grompp.cpp (line 1928)
Fatal error:
There were 36 errors in input file(s)
For more information and tips for troubleshooting, please check the GROMACS
website at Errors - Gromacs
-------------------------------------------------------
application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0
[unset]: write_line error; fd=-1 buf=:cmd=abort exitcode=1
:
system msg for write_line failure : Bad file descriptor
**~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~**
I checked the atoms for which ‘no default bonds types/ angles/ improper diherals’ were mentioned and it mainly involves the sulfotyrosine. I tried editing the ffbonded.itp file but could not understand how to do it. Kindly help me with this.