Fixing bugs in FF14SB port for Gromacs

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Bugs?

The newly released amber14sb made modifications for protein, DNA and RNA. This force field could be ported into gromacs as I already introduced previous.

However, there are some small bugs in the improper dihedral angles of HID, HIE and HIP.
So when generating tpr file, errors would be prompted.

When run grompp -f npt.mdp -p topol.top -c protein.gro -o product.tpr -n index, errors occur:

ERROR 1 [file topolff14sb_Protein_chain_B.itp, line 208041]:
  No default Improper Dih. types

The reason is that the parameters for some dihedral angles are missing. So we need to fix this.

How to fix?

Add the following two lines in the ffbonded.itp after the 730th lines:

NA  CW  CC  CT       4      180.00     4.60240     2     ;;; HID force field added
NA  CV  CC  CT       4      180.00     4.60240     2     ;;; HID force field added

The atom type CV and CW here are similar and share the same parameter value.

Save the file and run the command again, in general, errors won't exist anymore.

Comments

  1. Sifu15 November 2020 at 05:52

    Hi Zhang,

    I tried your solution in my ffbonded.itp file but below error occurred;

    ERROR 1 [file ffbonded.itp, line 731]:
    Not enough parameters


    ERROR 2 [file ffbonded.itp, line 732]:
    Not enough parameters

    Generated 3916 of the 3916 non-bonded parameter combinations
    Generating 1-4 interactions: fudge = 0.5
    Generated 3916 of the 3916 1-4 parameter combinations

    ERROR 3 [file system_Protein_chain_A.itp, line 33632]:
    No default Improper Dih. types

    Excluding 3 bonded neighbours molecule type 'Protein_chain_A'
    Excluding 3 bonded neighbours molecule type 'DNA_chain_B'
    Excluding 2 bonded neighbours molecule type 'SOL'

    NOTE 1 [file system.top, line 48]:
    System has non-zero total charge: -4.000000
    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.




    WARNING 1 [file system.top, line 48]:
    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 --- -------- --------


    There was 1 note

    There was 1 warning

    -------------------------------------------------------
    Program: gmx grompp, version 2020.4
    Source file: src/gromacs/gmxpreprocess/grompp.cpp (line 1928)

    Fatal error:
    There were 3 errors in input file(s)

    For more information and tips for troubleshooting, please check the GROMACS
    website at http://www.gromacs.org/Documentation/Errors
    -------------------------------------------------------

    Can you help?

    Best regards,
    Zul

    ReplyDelete

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