I got the error message below when carrying out protein in water simulation of a protein with the pub code: 3jzk
Fatal error:
Residue 1 named GLN of a molecule in the input file was mapped to an entry in the topology database, but the atom CG used in that entry is not found in the input file. Perhaps your atom and/or residue naming needs to be fixed
Please how do I fix this
If your input coordinate file has missing atoms, you need to model them back in with other software. GROMACS has no ability to repair side chains, fill missing gaps in loops, etc.
It was the x-ray structure that has the problem so I carried out pre-energy minimization with chimera USCF and later converted the structure into pdb using pymol there after I ignored H atoms when generating the protein topology and it worked…I am so grateful sir for being phenomenal
Sir is there any way that I can run MD analysis for an interrupted MD simulation…I was running a 10ns MD simulation of a protein with the pdb code 3jzk and the production run got terminated at about 4,100,000 nstep out of 5,000,000 nstep…I tried resuming from the last checkpoint file but the file was already corrupted so I would like to know if there is any chances for me to perform the analysis on the incomplete production run
Checkpoint files are written every 15 minutes, so if the current file is corrupted, use the one with “_prev” in its name to resume your simulation.
When I opened the one with preview using a text editor it was blank
Checkpoint files are binary. You can’t open them in a text editor.
Okay sir to resume I used the command gmx mdrun -v -s md.tpr -cpi md_prev.cpt -append
But it didn’t work
Sorry but “it didn’t work” isn’t anything anyone can possibly help with. What happened? Was there an error or unexpected behavior?
Alright sir I understand thank you
I have already include the ligand position restraint in the topol.top file and have used the make_ndx module to make the tc-grps group…in this case my ligand is denoted as LIG so in the nvt.mdp file I modified the tc-grps = Protein_LIG Water_and_ions
I used swissparam to generate the ligand topology and I am using the charmm36 ff
Sir I suspect this problem could be from my topol.top file in the file I defined the ligand molecule as ligand_c3 instead of LIG…could naming of the molecules in the [ molecule ] region of the topol.top file be this problem
Easiest and fastest way to find out is try it and see.
But which problem are you referring to here? There are at least two you have referred to in this topic.
If you want help with the:
Okay sir to resume I used the command gmx mdrun -v -s md.tpr -cpi md_prev.cpt -append
But it didn’t work
Then as Justin mentioned you need provide a lot more information. Copy and paste directly from the command line and text that is generated by GROMACS. What command did you run? What was the GROMACS error generated?
Hello sir could explain me a litle bit in detail how you fix this issue :
Residue 1 named GLN of a molecule in the input file was mapped to an entry in the topology database, but the atom CG used in that entry is not found in the input file. Perhaps your atom and/or residue naming needs to be fixed
Hello i’ve got this issue could you tell me with a little bit detail how fix your this is mine
Fatal error:
Residue 1 named VAL of a molecule in the input file was mapped
to an entry in the topology database, but the atom CG1 used in
that entry is not found in the input file. Perhaps your atom
and/or residue naming needs to be fixed.
Hello sir, i’ve got this issue could you tell me with a little bit detail how fix your this is mine
Fatal error:
Residue 1 named VAL of a molecule in the input file was mapped
to an entry in the topology database, but the atom CG1 used in
that entry is not found in the input file. Perhaps your atom
and/or residue naming needs to be fixed.