Hello, I am trying to follow the Protein-Ligand Complex tutorial but I end up in a problem
and I don’t understand what I am doing wrong.
I launch the command:
gmx editconf -f complex.gro -o newbox.gro -bt dodecahedron -d 1.0
That gives some output and a warning:
WARNING: Bad box in file complex.gro
Generated a cubic box 4.069 x 4.192 x 5.073
Read 2614 atoms
…
Then i use:
gmx solvate -cp newbox.gro -cs spc216.gro -p topol.top -o solv.gro
Generating solvent configuration
Will generate new solvent configuration of 5x5x3 boxes
Solvent box contains 37314 atoms in 12438 residues
Removed 3990 solvent atoms due to solvent-solvent overlap
Removed 2430 solvent atoms due to solute-solvent overlap
Sorting configuration
Found 1 molecule type:
SOL ( 3 atoms): 10298 residues
Generated solvent containing 30894 atoms in 10298 residues
Writing generated configuration to solv.gro
Back Off! I just backed up solv.gro to ./#solv.gro.2#
Output configuration contains 33508 atoms in 10461 residues
Volume : 341.949 (nm^3)
Density : 997.119 (g/l)
Number of solvent molecules: 10298
Processing topology
Adding line for 10298 solvent molecules with resname (SOL) to topology file (topol.top)
Back Off! I just backed up topol.top to ./#topol.top.7#
And, at last:
gmx grompp -f ions.mdp -c solv.gro -p topol.top -o ions.tpr
But here I get a fatal error:
Fatal error:
number of coordinates in coordinate file (solv.gro, 33508)
does not match topology (topol.top, 33530)
So, somewhere I am doing a mistake. But I did add the JZ4 in the topol.top under the [ molecules ].
I also added the coordinates of JZ4 in complex.gro (that originally is a copy of 3HTB_processed.gro) as described.
It is very difficult to help you. You just revived a four years old thread and you don’t give any information about what your problem is. I would guess that you will find answers to your question in the tutorial - take your time and read it carefully. Otherwise, it is probably not related to the issue in this thread, and in that case it would be better to start a new thread, carefully explaining your problem.
I find it and I corrected it but …it still gives the following problem:
Fatal error:
after gmx grompp -f ions.mdp -c solv.gro -p topol.top -o ions.tpr
i got
number of coordinates in coordinate file (solv.gro, 33518)
does not match topology (topol.top, 2636)
thank you in advance
There are very many threads with the same problem. You have probably forgotten to update the topol.top file when you added molecules (probably the solvent) to the .gro file. Read the tutorial carefully again.
Dear All, during the Preparation of the protein topology with pdb2gmx
I run : gmx pdb2gmx -f compp.pdb -o Cis_processed.gro -ter
I gives me → Fatal error:
Atom HH in residue ARG 2 was not found in rtp entry ARG with 25 atoms
while sorting atoms.
Thank you in advance