How to simulate a cyclic protein with AMBER99SB ff?

bee9
Wed, 08 Oct 2025 07:34:39 +0000
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Hello, I am trying to simulate a protein which I cyclized using Chimera. I have referred to the articles https://pubs.acs.org/doi/10.1021/acs.jpcb.4c00157 and followed this tutorial ( CP_tutorial/Tutorials at main · ysl-lab/CP_tutorial · GitHub ) for building the topology files. As per the tutorial, I have made the changes in the AMBER99SB forcefield files, topology file, PDB file, etc ( CP_tutorial/Tutorials/1. CP Building CPs Tutorial.docx at main · ysl-lab/CP_tutorial · GitHub and CP_tutorial/Tutorials/2. CP Cyclic Peptide Solvating and Equilibration.docx at main · ysl-lab/CP_tutorial · GitHub ). However, the energy minimization step is not working. Whether I use the RSFF2 forcefield (which the tutorial is better for cyclic proteins) or modified AMBER99SB forcefield, these are the errors that I got. Can you guide me to successfully complete the equilibration steps of a cyclic protein using AMBER99SB forcefield? This is because I want to simulate this cyclic protein with RNA using the AMBER99SB forcefield in future.

Error message 1

Command line: gmx_mpi grompp -f emin_pbc.mdp -c solvion.gro -p cycprotein_RSFF2.patched.top -o em.tpr Ignoring obsolete mdp entry ‘ns_type’ NOTE 1 [file emin_pbc.mdp]: You have set rlist larger than the interaction cut-off, but you also have verlet-buffer-tolerance > 0. Will set rlist using verlet-buffer-tolerance. Setting the LD random seed to -90382721 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 cycprotein_RSFF2.patched.top, line 2715]: No default Bond types Excluding 3 bonded neighbours molecule type ‘Protein_chain_A’ NOTE 2 [file cycprotein_RSFF2.patched.top, line 13014]: System has non-zero total charge: -4.000000 Total charge should normally be an integer. See Floating point arithmetic — GROMACS webpage https://www.gromacs.org documentation for discussion on how close it should be to an integer. WARNING 1 [file cycprotein_RSFF2.patched.top, line 13014]: You are using Ewald electrostatics in a system with net charge. This can lead to severe artifacts, such as ions moving into regions with low dielectric, due to the uniform background charge. We suggest to neutralize your system with counter ions, possibly in combination with a physiological salt concentration. ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ J. S. Hub, B. L. de Groot, H. Grubmueller, G. Groenhof Quantifying Artifacts in Ewald Simulations of Inhomogeneous Systems with a Net Charge J. Chem. Theory Comput. 10 (2014) pp. 381-393 -------- -------- — Thank You — -------- -------- ------------------------------------------------------- Program: gmx grompp, version 2020-UNCHECKED Source file: src/gromacs/gmxpreprocess/grompp.cpp (line 668) Fatal error: number of coordinates in coordinate file (solvion.gro, 25738) does not match topology (cycprotein_RSFF2.patched.top, 1293) For more information and tips for troubleshooting, please check the GROMACS website at Common Errors — GROMACS webpage https://www.gromacs.org documentation ------------------------------------------------------- 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 [user@login07 local_gmx_library]$

Error message 2

GROMACS: gmx grompp, version 2020-UNCHECKED Executable: /home/apps/gromacs_2020/bin/gmx_mpi Data prefix: /home/apps/gromacs_2020 Working dir: /scratch/cyc-protein/local_gmx_library Command line: gmx_mpi grompp -f emin_vac.mdp -c cyc_prot.gro -p cycprotein_RSFF2.patched.top -o vac.tpr ERROR 1 [file emin_vac.mdp]: With Verlet lists only full pbc or pbc=xy with walls is supported Setting the LD random seed to -1474596854 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 2 [file cycprotein_RSFF2.patched.top, line 2715]: No default Bond types Excluding 3 bonded neighbours molecule type ‘Protein_chain_A’ NOTE 1 [file cycprotein_RSFF2.patched.top, line 13014]: System has non-zero total charge: -4.000000 Total charge should normally be an integer. See Floating point arithmetic — GROMACS webpage https://www.gromacs.org documentation for discussion on how close it should be to an integer. There was 1 note ------------------------------------------------------- Program: gmx grompp, version 2020-UNCHECKED Source file: src/gromacs/gmxpreprocess/grompp.cpp (line 1927) Fatal error: There were 2 errors in input file(s) For more information and tips for troubleshooting, please check the GROMACS

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