Topol.top does not exist

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Hi guys,

I created a silica surface on CHARMM-GUI and downloaded the tgz files. This was unzipped and then I unzipped the tar file to receive the charmm-gui file and within this I accessed the gromacs file and this contained the following files.

-README
-mdout.mdp
-step3_input.gro
-step3_input.pdb
-step3_input.psf
-step4.0_minimization.mdp
-step4.1_equilibration.mdp
-step5_production.mdp
-topol.top
-toppar

I then opened the README file and obtained the following commands for Ubuntu.

Minimisation

gmx grompp -f step4.0_minimization.mdp -o step4.0_minimization.tpr -c step3_input.gro -r step3_input.gro -p topol.top -maxwarn 1
gmx mdrun -v -deffnm step4.0_minimization

Equilibration

gmx grompp -f step4.1_equilibration.mdp -o step4.1_equilibration.tpr -c step4.0_minimization.gro -r step3_input.gro -p topol.top
gmx mdrun -v -deffnm step4.1_equilibration

Production

gmx grompp -f step5_production.mdp -o step5_.tpr -cstep4.1_equilibration.gro -p topol.top
gmx mdrun -v -deffnm step5_

I obtain an md.out file for the minimisation step with an initial warning about the input file. I the try to carry out the md run but get the message that my topol file does not exist despite it being present within the directory.

What is the issue?

I really would appreciate a response as I have been trying to rectify this issue for a day with no avail. I desperately needed to overcome this issue to continue with my simulation. Any help would be really appreciated.

Is this the same “missing topol” error that your other thread is about? Or is this a distinct issue? Again, please provide the entire error message, copied and pasted from the terminal.

This is the first error I get when I insert the minimisation command line.

  • Program: gmx grompp, version 2020.1-Ubuntu-2020.1-1
  • Source file: src/gromacs/gmxpreprocess/grompp.cpp (line 1928)
  • Fatal error: There was 1 error in input file(s)

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

I then carry out the mdrun.

gmx mdrun -v -deffnm step4.0_minimization

  • Program: gmx mdrun, version 2020.1-Ubuntu-2020.1-1
  • Source file: src/gromacs/options/options.cpp (line 179)
  • Function: void gmx::internal::OptionSectionImpl::finish()
  • Error in user input: Invalid input values. In option s - Required option was not provided, and the default file ‘topol’ does not exist or is not accessible.
  • The following extensions were tried to complete the file name: .tpr

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

I obtain an mdout.mdp file.

I then tried to continue with the equilibration step.

gmx grompp -f step4.1_equilibration.mdp -o step4.1_equilibration.tpr -c step4.0_minimization.gro -r step3_input.gro -p topol.top

  • Program: gmx grompp, version 2020.1-Ubuntu-2020.1-1
  • Source file: src/gromacs/commandline/cmdlineparser.cpp (line 275)
  • Function: void gmx::CommandLineParser::parse(int*, char**)
  • Error in user input:
  • Invalid command-line options. In In command-line option -c
  • File ‘step4.0_minimization.gro’ does not exist or is not accessible. The file could not be opened
  • Reason: No such file or directory (call to fopen() returned error code 2)
    For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors

I assume I do not have the minimisation.gro because it is not generated from the previous command lines in order for me to carry out the next step. What is the issue?

Your help would be greatly appreciated.

Many Thanks,

Amo

“Fatal error” means nothing after that will work and you never got the first .tpr file. So again I ask, what was the error in the first step? It will have been printed to the screen and labeled very clearly.

These are the details following the first command for minimisation.

  • GROMACS: gmx grompp, version 2020.1-Ubuntu-2020.1-1
  • Executable: /usr/bin/gmx
  • Data prefix: /usr
  • Working dir: /mnt/c/Users/Ahmod/MD/Project/silicapH7/charmm-gui-9864677367/gromacs
  • Command line: gmx grompp -f step4.0_minimization.mdp -o step4.0_minimization.tpr -c step3_input.gro -r step3_input.gro -p topol.top
  • Setting the LD random seed to 572217900
  • Generated 28 of the 28 non-bonded parameter combinations
  • Generating 1-4 interactions: fudge = 1
  • Generated 0 of the 28 1-4 parameter combinations
  • Excluding 3 bonded neighbours molecule type ‘NMA’ turning H bonds into constraints… Excluding 1 bonded neighbours molecule type ‘NMB’ turning H bonds into constraints… Excluding 2 bonded neighbours molecule type ‘TIP3’ turning H bonds into constraints… WARNING 1 [file topol.top, line 24]:
  • The following macros were defined in the ‘define’ mdp field with the -D prefix, but were not used in the topology: DIHRES POSRES_FC_SC DIHRES_FC
  • If you haven’t made a spelling error, either use the macro you defined, or don’t define the macro ERROR 1 [file topol.top, line 24]: ERROR: The cut-off length is longer than half the shortest box vector or longer than the smallest box diagonal element. Increase the box size or decrease rlist. There was 1 warning

The parameters for my system was solvate, 80x80x10 box size, periodic boundaries in x and y only, choose 4 nm to edge, add neutralising ions.

In what units? Å as is the default in CHARMM-GUI? If so, you have a 1-nm (10 Å) z-dimension, which is too small and triggers the fatal error.

I have kept the box size the same and change the edge distance to 10 nm. I downloaded the files and no longer have this issue. Also, I would like to know how do I change the charges of a protein using Gromacs?

Do I use the -ter command and what would be the command line?

Change charges? You want to alter the protonation state? There are options in pdb2gmx to do that; -ter only affects the protonation of the terminal groups but nothing else.

I would like my protein to resemble the charges of the side chains at pH7 and would like the aspartic and glutamic acid to be negatively charged. Also, the lysine, arginine, histidine to be positively charged.

gmx pdb2gmx -f 1GUJAB.pdb -o insulin_processed.gro -water spce - asp - glu - lys - arg - his -

Would this be the correct command line?

pdb2gmx already assigns the canonical protonation states for pH 7. You don’t need to assign them manually as you will just be selecting all the defaults. Histidine is an interesting case because pdb2gmx searches for hydrogen bonding partners in determining whether each His is δ- or ε-protonated or is formally charged. A positive His is not the dominant form at neutral pH so I do not understand why you would want them set that way; only when participating in certain interactions will His be more likely to carry a positive charge at pH 7.

I have realised that I do not need to adjust anything for pH 7. However, if I were to assign the charges at side chains at different pH. For example, at pH 2 - then what would be the generic command line using pdb2gmx or how would I issue this command in gromacs?

gmx pdb2gmx -inter

gmx pdb2gmx -inter - is then followed by the amino acids I would like to assign at a certain pH?

e.g. gmx pdb2gmx -inter -lys as it has a positive charge at pH 2 as simple example?

No. -inter is its own option that allows you to specify all protonation states. Please see the pdb2gmx help information.

I have changed the charges in order it to mimic the conditions of insulin molecule for pH 3 and pH 5.6 and I generated these PDB files at their respective pH’s using CHARMM Gui. In order to mimic the assigned charges at these pH values I did the following gmx pdb2gmx command.

gmx pdb2gmx -f 1GUJAB.pdb -o insulin_processed.gro -glu - his

  • Processing chain 1 ‘A’ (163 atoms, 21 residues)
  • Which GLUTAMINE type do you want for residue 5?
  • I chose 1. Protonated (charge +1) (QLN)
  • Which GLUTAMINE type do you want for residue 15?
  • I chose 1. Protonated (charge +1) (QLN)
  • Which GLUTAMIC ACID type do you want for residue 4?
  • I chose 1. Protonated (charge 0) (GLUH)
  • Which GLUTAMIC ACID type do you want for residue 17?
  • I chose 1. Protonated (charge 0) (GLUH)
  • Link CYS-6 SG-43 and CYS-11 SG-76 (for the disulphide bond)
  • I selected n
  • Select start terminus type for GLY-1
  • 2: None
  • Select end terminus type for ASN-21
  • 2: None
  • Which histidine type do you want for residue 5?
  • I chose 1. H on NE2 only (HISB)
  • Which histidine type do you want for residue 10?
  • I chose 1. H on NE2 only (HISB)

However, it offers to protonate Glutamines but these do not get protonated at all.Instead it should offer to change 4 glutamic acids on chains A and B in positions 4, 17 (A) and 13,21 (B) but I do not get this offer.

Also, I wanted to change the CTER of the A chain to CNEU of my insulin molecule but my way of doing this was using CHARMM but this obviously does not mix well with Gromos and I get an error for the input file. Is there a way of manipulating the PDB to make this change?

Also, I would like to protonate the Histidines at pH 5.6 but are these done automatically? I issued the following command and changed the protonation states of Histidine for both chain A and B but is this done automatically? I have read that this does not need to be issued.

Lastly, I think the protonation states between pH 7 - 9 take care of themselves and charge states do not need to be specifically issued using pdb2gmx command for my PDB of insulin at pH 9.

If you could provide any advice or explanation on these questions, I would really appreciated.

Thank you.

I don’t know why you would protonate Gln residues anyway. Its pKa is < 1.

CHARMM supports a neutral terminus, either CNEU in CHARMM or COOH in the GROMACS port.

You can change His protonation like any other titratable group, and at pH 5.6, some of them may be fully protonated.