# Some pdb files can not work via GROMACS **URL:** \ **Category:** User discussions\ **Created:** [August 5, 2023, 7:05pm UTC](https://gromacs.bioexcel.eu/t/some-pdb-files-can-not-work-via-gromacs/6969 "2023-08-05T19:05:59Z")\ **Posts on this page:** 3\ **Page:** 1
**Author:** ![pelinsu](https://avatars.discourse-cdn.com/v4/letter/p/5fc32e/32.png) [@pelinsu](https://gromacs.bioexcel.eu/u/pelinsu)\ **Post date:** [August 5, 2023, 7:05pm UTC](https://gromacs.bioexcel.eu/t/some-pdb-files-can-not-work-via-gromacs/6969/1 "2023-08-05T19:05:59Z")
GROMACS version: GROMACS modification: Yes/No Here post your question Hi all, i am a new person for GROMACS. when I try to use tutorial 5(protein-ligand complex) I had some weird error in the topology and energy minimization part. originally my protein has 7 chains but I want to use only 2 chains of 7 chains. before to start gromacs I made some preprocess via chimera (I deleted solvent, ligand and other 5 chains). but when I try to make topol.top I got this error: Fatal error: Atom HB3 in residue MET 1 was not found in rtp entry MET with 19 atoms while sorting atoms. For a hydrogen, this can be a different protonation state, or it might have had a different number in the PDB file and was rebuilt (it might for instance have been H3, and we only expected H1 & H2). Note that hydrogens might have been added to the entry for the N-terminus. Remove this hydrogen or choose a different protonation state to solve it. Option -ignh will ignore all hydrogens in the input. and later on, I used -ignh but in that case my topol.top file does not seems well. it seems: This is a standalone topology file ; ; Created by: ; :-) GROMACS - gmx pdb2gmx, 2021.4-Homebrew (-: ; ; Executable: /usr/local/bin/…/Cellar/gromacs/2021.4/bin/gmx ; Data prefix: /usr/local/bin/…/Cellar/gromacs/2021.4 ; Working dir: /Users/…/Desktop/kodaMD ; Command line: ; gmx pdb2gmx -f …pdb -o …\_processed.gro -ter -ignh ; Force field was read from the standard GROMACS share directory. ; ; Include forcefield parameters #include “charmm27.ff/forcefield.itp” ; Include ligand parameters #include “LIG.itp” ; Include chain topologies #include “topol\_Protein\_chain\_A.itp” #include “topol\_Protein\_chain\_B.itp” ; Include water topology #include “charmm27.ff/tip3p.itp” #ifdef POSRES\_WATER ; Position restraint for each water oxygen [position\_restraints] ; i funct fcx fcy fcz 1 1 1000 1000 1000 #endif ; Include topology for ions #include “charmm27.ff/ions.itp” [system] ; Name Protein in water [molecules] ; Compound #mols Protein\_chain\_A 1 Protein\_chain\_B 1 LIG 1 SOL 24721 ---
**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:** [August 6, 2023, 3:00am UTC](https://gromacs.bioexcel.eu/t/some-pdb-files-can-not-work-via-gromacs/6969/2 "2023-08-06T03:00:24Z")
That’s a normal topology for a multi-chain system. `pdb2gmx` will, by default, write the topology of each protein chain to its own `.itp` file. Note that if you are using the tutorial’s approach to parametrize the ligand with CGenFF, it will not work in conjunction with the `charmm27.ff` files provided with GROMACS. You need to get the CHARMM36 port from Alex MacKerell’s site and generate the protein topology with that. ---
**Author:** ![pelinsu](https://avatars.discourse-cdn.com/v4/letter/p/5fc32e/32.png) [@pelinsu](https://gromacs.bioexcel.eu/u/pelinsu)\ **Post date:** [October 2, 2023, 8:26am UTC](https://gromacs.bioexcel.eu/t/some-pdb-files-can-not-work-via-gromacs/6969/3 "2023-10-02T08:26:36Z")
Hi, thank you. I am always getting rmsd graphs that have very fluctuated for both protein or protein-ligand simulations.when I checked via VMD I realized dimers are separated from each other. if I add posre.A.itp and posre.B.itp lines for my topology files, is it work or not needed ? if it is not needed how can I solve? this is protein in water for 50 ns ![Screenshot 2023-09-30 at 13.17.45](https://europe1.discourse-cdn.com/flex017/uploads/bioexcel1/original/2X/9/9536366fb9c9e8253b8c86665ea7c5a386426b50.png) this is protein-ligand for 5 ns ![WhatsApp Image 2023-10-02 at 09.54.48](https://europe1.discourse-cdn.com/flex017/uploads/bioexcel1/original/2X/e/e54af7b7d88ec35539802cfe891bfef0ee3b995e.jpeg) this protein-ligand for 100 ns ![Screenshot 2023-09-30 at 14.04.24](https://europe1.discourse-cdn.com/flex017/uploads/bioexcel1/original/2X/1/19337da6545c5187e2476be47c3e6001e63be6cd.png)