Hi Eric, I would like to know more about how do you assign chain letters to the chains. I have noticed that when the initial structure is not perfect enough, the number of chains is increasing during the progress of simulation in individual GRO files. The extra chains have usually only one or a low number of residues. I was thinking that this occurs because the residues get separated too much during the simulation (for instance it occurred when the GROMACS minimization was performed in single precision or when there were many LINCS errors during minimization). But now I have a case when the initial GRO file prepared by CHARMM-GUI has a broken chain but after minimization the resulting GRO file has intact chains which is puzzling to me. When I open a trajectory in the old Chimera, I always get the correct number and contents of chains. I have attached a zip file with two examples, in which the files TPR and XTC opened in Chimera give a structure with complete chains A-D but the equivalent GRO file open in ChimeraX has broken files. In the PDBs I have deleted all residues except the original protein structure with ligands. step7_1_Chimera.pdb - beginning of the simulation, TPR and XTC open with Chimera for frames 1-10, frame 1 shown step7_1_ChimeraX.pdb - beginning of the production run, first GRO open with ChimeraX, which corresponds to the first frame step7_1000_Chimera.pdb - end of the simulation, TPR and XTC open with Chimera for frames 991-1000 (the last TPR file), frame 10 shown step_100_GRO_ChimeraX.pdb - end of the simulation, last GRO open with ChimeraX, which corresponds to the last frame. step7_1000_trjctr_ChimeraX.pdb - end of the simulation, frame 1000 of the combined trajectory open after centering the protein in GROMACS. It can be seen that (1) the RMSD between the C-alpha atoms of PDBs corresponding to the same frame is ~ 0; and (2) the last frame is still quite OK in the step7_1000_trjctr_ChimeraX.pdb, but since no GRO file in the whole series was unbroken, it cannot be repaired in ChimeraX. Thanks in advance for feedback. Best regards Sasha -----Original Message----- From: Eric Pettersen [mailto:pett@cgl.ucsf.edu] Sent: Thursday, April 24, 2025 02:28 To: Alexandra Zahradnikova Cc: ChimeraX Users Help Subject: Re: [chimerax-users] Labeling chains in MD simulation trajectories of a multimer Hi Alexandra, Thanks for the example file. I have committed changes to .gro file reading to do a better job of identifying chains and assigning chain IDs. In your example file, the four protein chains are assigned chain IDs A-D and all the singleton residues get chain ID E. The fix will be in the next daily build. --Eric
On Apr 22, 2025, at 1:01 PM, Alexandra Zahradnikova <Alexandra.Zahradnikova@savba.sk> wrote:
Hi Eric Sorry, I have sent the unfinished mail by mistake, but you got the problem perfectly. Since I need to analyze e.g. RMSD/RMSF or H-bonds per chain, I need to have different names for the four chains. I can do it in old Chimera, because it requires a combination of a TPR and an XTC file, which will produce the correct chain names. However ChimeraX reads only the GRO file but not the TPR file, and the GRO file does not seem to have this information. I attach a sample .gro file with the following .xtc trajectory. In the .gro file, everything including protein, ions, lipids, and water is one "principal chain" without a name. I have also added the .tpr file so you can compare the result in ChimeraX and Chimera. Best Sasha
-----Original Message----- From: Eric Pettersen [mailto:pett@cgl.ucsf.edu] Sent: Tuesday, April 22, 2025 7:12 PM To: Alexandra Zahradnikova Cc: ChimeraX Users Help Subject: Re: [chimerax-users] Labeling chains in MD simulation trajectories of a multimer
Hi Alexandra, I don't actually have access to any .gro files that have multiple chains. If you could send me an example I might be able to improve ChimeraX's behavior in that situation.
--Eric
Eric Pettersen UCSF Computer Graphics Lab
On Apr 22, 2025, at 7:23 AM, Alexandra Zahradnikova via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi All, I am interested in MD simulations of homomultimeric ion channels, which I do in GROMACS. I would like to analyze my output files with ChimeraX but I run into the following problem: The .gro output of the simulation consists of a single chain named /? in ChimeraX. When I open the file in old Chimera, it shows every chain of the original protein separately but with the same name ()
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