# Fatal error: Residue 1 named GLN of a molecule in the input file was mapped to an entry in the topol **URL:** \ **Category:** User discussions\ **Created:** [September 1, 2020, 11:14am UTC](https://gromacs.bioexcel.eu/t/fatal-error-residue-1-named-gln-of-a-molecule-in-the-input-file-was-mapped-to-an-entry-in-the-topol/751 "2020-09-01T11:14:45Z")\ **Posts on this page:** 17\ **Page:** 1
**Author:** ![Ponaskillz](https://avatars.discourse-cdn.com/v4/letter/p/ecccb3/32.png) [@Ponaskillz](https://gromacs.bioexcel.eu/u/Ponaskillz)\ **Post date:** [September 1, 2020, 11:14am UTC](https://gromacs.bioexcel.eu/t/fatal-error-residue-1-named-gln-of-a-molecule-in-the-input-file-was-mapped-to-an-entry-in-the-topol/751/1 "2020-09-01T11:14:45Z")
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 ---
**Author:** ![jalemkul](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/jalemkul/32/18_2.png) [@jalemkul](https://gromacs.bioexcel.eu/u/jalemkul)\ **Post date:** [September 1, 2020, 5:27pm UTC](https://gromacs.bioexcel.eu/t/fatal-error-residue-1-named-gln-of-a-molecule-in-the-input-file-was-mapped-to-an-entry-in-the-topol/751/2 "2020-09-01T17:27:19Z")
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. ---
**Author:** ![Ponaskillz](https://avatars.discourse-cdn.com/v4/letter/p/ecccb3/32.png) [@Ponaskillz](https://gromacs.bioexcel.eu/u/Ponaskillz)\ **Post date:** [September 3, 2020, 9:44am UTC](https://gromacs.bioexcel.eu/t/fatal-error-residue-1-named-gln-of-a-molecule-in-the-input-file-was-mapped-to-an-entry-in-the-topol/751/3 "2020-09-03T09:44:28Z")
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 ---
**Author:** ![Ponaskillz](https://avatars.discourse-cdn.com/v4/letter/p/ecccb3/32.png) [@Ponaskillz](https://gromacs.bioexcel.eu/u/Ponaskillz)\ **Post date:** [September 20, 2020, 6:15pm UTC](https://gromacs.bioexcel.eu/t/fatal-error-residue-1-named-gln-of-a-molecule-in-the-input-file-was-mapped-to-an-entry-in-the-topol/751/4 "2020-09-20T18:15:13Z")
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 ---
**Author:** ![jalemkul](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/jalemkul/32/18_2.png) [@jalemkul](https://gromacs.bioexcel.eu/u/jalemkul)\ **Post date:** [September 21, 2020, 1:24am UTC](https://gromacs.bioexcel.eu/t/fatal-error-residue-1-named-gln-of-a-molecule-in-the-input-file-was-mapped-to-an-entry-in-the-topol/751/5 "2020-09-21T01:24:45Z")
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. ---
**Author:** ![Ponaskillz](https://avatars.discourse-cdn.com/v4/letter/p/ecccb3/32.png) [@Ponaskillz](https://gromacs.bioexcel.eu/u/Ponaskillz)\ **Post date:** [September 23, 2020, 9:55am UTC](https://gromacs.bioexcel.eu/t/fatal-error-residue-1-named-gln-of-a-molecule-in-the-input-file-was-mapped-to-an-entry-in-the-topol/751/6 "2020-09-23T09:55:48Z")
When I opened the one with preview using a text editor it was blank ---
**Author:** ![jalemkul](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/jalemkul/32/18_2.png) [@jalemkul](https://gromacs.bioexcel.eu/u/jalemkul)\ **Post date:** [September 23, 2020, 10:07am UTC](https://gromacs.bioexcel.eu/t/fatal-error-residue-1-named-gln-of-a-molecule-in-the-input-file-was-mapped-to-an-entry-in-the-topol/751/7 "2020-09-23T10:07:08Z")
Checkpoint files are binary. You can’t open them in a text editor. ---
**Author:** ![Ponaskillz](https://avatars.discourse-cdn.com/v4/letter/p/ecccb3/32.png) [@Ponaskillz](https://gromacs.bioexcel.eu/u/Ponaskillz)\ **Post date:** [September 23, 2020, 12:37pm UTC](https://gromacs.bioexcel.eu/t/fatal-error-residue-1-named-gln-of-a-molecule-in-the-input-file-was-mapped-to-an-entry-in-the-topol/751/8 "2020-09-23T12:37:45Z")
Okay sir to resume I used the command gmx mdrun -v -s md.tpr -cpi md\_prev.cpt -append But it didn’t work ---
**Author:** ![jalemkul](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/jalemkul/32/18_2.png) [@jalemkul](https://gromacs.bioexcel.eu/u/jalemkul)\ **Post date:** [September 23, 2020, 1:32pm UTC](https://gromacs.bioexcel.eu/t/fatal-error-residue-1-named-gln-of-a-molecule-in-the-input-file-was-mapped-to-an-entry-in-the-topol/751/9 "2020-09-23T13:32:28Z")
Sorry but “it didn’t work” isn’t anything anyone can possibly help with. What happened? Was there an error or unexpected behavior? ---
**Author:** ![Ponaskillz](https://avatars.discourse-cdn.com/v4/letter/p/ecccb3/32.png) [@Ponaskillz](https://gromacs.bioexcel.eu/u/Ponaskillz)\ **Post date:** [September 23, 2020, 1:48pm UTC](https://gromacs.bioexcel.eu/t/fatal-error-residue-1-named-gln-of-a-molecule-in-the-input-file-was-mapped-to-an-entry-in-the-topol/751/10 "2020-09-23T13:48:59Z")
Alright sir I understand thank you ---
**Author:** ![Ponaskillz](https://avatars.discourse-cdn.com/v4/letter/p/ecccb3/32.png) [@Ponaskillz](https://gromacs.bioexcel.eu/u/Ponaskillz)\ **Post date:** [September 26, 2020, 6:01am UTC](https://gromacs.bioexcel.eu/t/fatal-error-residue-1-named-gln-of-a-molecule-in-the-input-file-was-mapped-to-an-entry-in-the-topol/751/11 "2020-09-26T06:01:17Z")
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 ---
**Author:** ![Ponaskillz](https://avatars.discourse-cdn.com/v4/letter/p/ecccb3/32.png) [@Ponaskillz](https://gromacs.bioexcel.eu/u/Ponaskillz)\ **Post date:** [September 26, 2020, 6:12am UTC](https://gromacs.bioexcel.eu/t/fatal-error-residue-1-named-gln-of-a-molecule-in-the-input-file-was-mapped-to-an-entry-in-the-topol/751/12 "2020-09-26T06:12:53Z")
I used swissparam to generate the ligand topology and I am using the charmm36 ff ---
**Author:** ![Ponaskillz](https://avatars.discourse-cdn.com/v4/letter/p/ecccb3/32.png) [@Ponaskillz](https://gromacs.bioexcel.eu/u/Ponaskillz)\ **Post date:** [September 26, 2020, 6:16am UTC](https://gromacs.bioexcel.eu/t/fatal-error-residue-1-named-gln-of-a-molecule-in-the-input-file-was-mapped-to-an-entry-in-the-topol/751/13 "2020-09-26T06:16:00Z")
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 ---
**Author:** ![Dr\_DBW](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/dr_dbw/32/42_2.png) [@Dr\_DBW](https://gromacs.bioexcel.eu/u/Dr_DBW)\ **Post date:** [September 28, 2020, 7:04am UTC](https://gromacs.bioexcel.eu/t/fatal-error-residue-1-named-gln-of-a-molecule-in-the-input-file-was-mapped-to-an-entry-in-the-topol/751/14 "2020-09-28T07:04:09Z")
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? ---
**Author:** ![Sakho](https://avatars.discourse-cdn.com/v4/letter/s/9de0a6/32.png) [@Sakho](https://gromacs.bioexcel.eu/u/Sakho)\ **Post date:** [September 23, 2024, 11:18am UTC](https://gromacs.bioexcel.eu/t/fatal-error-residue-1-named-gln-of-a-molecule-in-the-input-file-was-mapped-to-an-entry-in-the-topol/751/15 "2024-09-23T11:18:26Z")
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 ---
**Author:** ![Sakho](https://avatars.discourse-cdn.com/v4/letter/s/9de0a6/32.png) [@Sakho](https://gromacs.bioexcel.eu/u/Sakho)\ **Post date:** [September 27, 2024, 10:10am UTC](https://gromacs.bioexcel.eu/t/fatal-error-residue-1-named-gln-of-a-molecule-in-the-input-file-was-mapped-to-an-entry-in-the-topol/751/16 "2024-09-27T10:10:04Z")
Hello i’ve got this issue could you tell me with a little bit detail how fix your this is mine ```auto 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. ``` ---
**Author:** ![Sakho](https://avatars.discourse-cdn.com/v4/letter/s/9de0a6/32.png) [@Sakho](https://gromacs.bioexcel.eu/u/Sakho)\ **Post date:** [September 27, 2024, 10:11am UTC](https://gromacs.bioexcel.eu/t/fatal-error-residue-1-named-gln-of-a-molecule-in-the-input-file-was-mapped-to-an-entry-in-the-topol/751/17 "2024-09-27T10:11:11Z")
Hello sir, i’ve got this issue could you tell me with a little bit detail how fix your this is mine ```auto 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. ```