KALP tutorial 2: pack the lipids with helix, grompp fatal error

User discussions
1

GROMACS version:2020.3
GROMACS modification: No

Hell everyone,
I am new to MD simulation. I was just going through the gromacs tutorial 2: KALP15 in DPPC. In part II: 2. Pack the lipids around the protein, after executing expansion command:
perl inflategro.pl system.gro 4 DPPC 14 system_inflated.gro 5 area.dat

two DPPC lipids had been removed, so i added the text: “DPPC 126” into the last line of topol.top file (931 line) :

[ molecules ]
; Compound        #mols
Protein             1
DPPC                126

During energy minimization step:
gmx grompp -f minim_inflategro.mdp -c system_inflated.gro -p topol.top -r system_inflated.gro -o system_inflated_em.tpr

i faced a fatal error:

GROMACS:      gmx grompp, version 2020.3
Executable:   /usr/local/gromacs/bin/gmx
Data prefix:  /usr/local/gromacs
Working dir:  /mnt/c/Users/hye/Desktop/MDS/tutorial 2
Command line:
  gmx grompp -f minim_inflategro.mdp -c system_inflated.gro -p topol.top -r system_inflated.gro -o system_inflated_em.tpr

Ignoring obsolete mdp entry 'ns_type'

NOTE 1 [file minim_inflategro.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 1595602430
Generated 813 of the 2346 non-bonded parameter combinations
Excluding 3 bonded neighbours molecule type 'Protein'
Excluding 3 bonded neighbours molecule type 'DPPC'

WARNING 1 [file topol.top, line 932]:
  The GROMOS force fields have been parametrized with a physically
  incorrect multiple-time-stepping scheme for a twin-range cut-off. When
  used with a single-range cut-off (or a correct Trotter
  multiple-time-stepping scheme), physical properties, such as the density,
  might differ from the intended values. Since there are researchers
  actively working on validating GROMOS with modern integrators we have not
  yet removed the GROMOS force fields, but you should be aware of these
  issues and check if molecules in your system are affected before
  proceeding. Further information is available at
  https://redmine.gromacs.org/issues/2884 , and a longer explanation of our
  decision to remove physically incorrect algorithms can be found at
  https://doi.org/10.26434/chemrxiv.11474583.v1 .


NOTE 2 [file topol.top, line 932]:
  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.



Analysing residue names:
There are:    17    Protein residues
There are:   126      Other residues
Analysing Protein...
Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...
Number of degrees of freedom in T-Coupling group rest is 19311.00

NOTE 3 [file minim_inflategro.mdp]:
  Removing center of mass motion in the presence of position restraints
  might cause artifacts. When you are using position restraints to
  equilibrate a macro-molecule, the artifacts are usually negligible.


NOTE 4 [file minim_inflategro.mdp]:
  You are using a plain Coulomb cut-off, which might produce artifacts.
  You might want to consider using PME electrostatics.


This run will generate roughly 1 Mb of data

There were 4 notes

There was 1 warning

-------------------------------------------------------
Program:     gmx grompp, version 2020.3
Source file: src/gromacs/gmxpreprocess/grompp.cpp (line 2353)

Fatal error:
Too many warnings (1).
If you are sure all warnings are harmless, use the -maxwarn option.

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

following the above instruction, i try to use the -maxwarn option, but did not solve the problem:

Command line:
  gmx grompp -f minim_inflategro.mdp -c system_inflated.gro -p topol.top -r system_inflated.gro -o system_inflated_em.tpr -maxwarn


-------------------------------------------------------
Program:     gmx grompp, version 2020.3
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 command-line option -maxwarn
    Too few (valid) values

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

after that, i don’t know how to solve this warning, please help, i am new to gromacs, many thanks

2

Hi,
the option “-maxwarn” should be followed by an integer number. In your specific case
-maxwarn 1 .

Please note that one has to be very careful in using the option -maxwarn. This option set the number of allowed warnings during input processing. Thus it should not use for normal use. And one should be aware of what it is ignoring.

regards

3

thank you! it successfully generate system_inflated_em.tpr file.