Program: gmx pdb2gmx, version 2021.4-Ubuntu-2021.4-2
Source file: src/gromacs/gmxpreprocess/resall.cpp (line 597)
Fatal error:
Residue ‘DOP’ not found in residue topology database
For more information and tips for troubleshooting, please check the GROMACS
website at Common Errors — GROMACS webpage https://www.gromacs.org documentation
Can anyone help me . I have already visit the documentation but could not find . Thanks in advance
Did you parametrize this residue (DOP) into an .rtp entry? It doesn’t look like a standard residue.
Hi milosz.weeczor
this is not a standared residue I take for DOPC molecules. but can you please tell me about how to parameterized the DOP into .rty entry
I recently made a tutorial for creating .rtp entries with Gromologist, or incorporating ligands parametrized elsewhere into Gromacs, you might want to take a look:
Either way, unless a parametrization is available somewhere already, you’ll need to parameterize the ligand externally, either following your chosen force field’s protocol or using established webservers, such as CHARMM-GUI/CGenFF or Acpype/GAFF.
We have no idea what you are doing, as per the response i can see that the molecule is DOPC which i assume lipid. Which forcefield you are using? providing more details can understand the issue and help you better.
hello Scinikhil
I am doing the MD simulation of phospholipids and glycolipids … I have generated the bilayer structure for phospholipids and glycolipids with the help of packmol, for glycolipids my molecule is b-glucose while for phospholipids is dopc … for glycolipids, I give residue name Glu while for DOPC molecules residue name is Dop…
bilayer constitutes a total number of 300 molecules … now when I am doing the MD simulation while using the first command gmx pdb2gmx … shows me these errors. so this is the whole story
hellow milosz…
Can u please tell me how to parameterized the residue into an .rtp entry …
explain ?
If DOP is literally identical to DOPC, you don’t need to parameterize anything, just find a force field that supports the lipids you need. For CHARMM, people often use the Membrane Builder server tool to obtain a complete assembled system + validated topology. If it’s Amber and its Slipids, here’s one place you can get the force field from, although I see you will have to merge e.g. the .rtp files for DOPG (tails) and POPC (head) to obtain DOPC.
see here
hellow milosz.wieczor
I have already used the membrane builder to generate the structure … after that, I made some corrections in the structure like removing some tails that were not required after that edit the .itp files of both phospholipids and glycolipids according to my original bilayer pdb files but when here I used the modified .itp files in the gromac still did not work… can you please tell me more about .rtp file?
Hi Fayaz,
CHARMM-GUI is set up in such a way that you should include all the modifications within the workflow. If you introduce modifications to the final setup, you have to either describe exactly what you modified, or learn the logic of Gromacs to make sure your modifications make sense. From what you’ve said so far it’s impossible to know what might be causing your problem.
sir,
the main problem which I face is that what charm GUI generated structure is different compared to my structure because in the charm GUI generated structure there were few extra ester linkages and also tail size is different because I am doing with tail size C10C8 but charm GUI gives me C14C14 also with extra ester linkage after that I modified their .itp files i.e removing the extra tails and ester linkage, renumbering their position, accordingly my original pdb now when put this commands gmx x2top -f input.pdb -o output.gro -ignh -ter -water spc so give me the same errors .
although I copied the .itp and pasted it into the folder of forcefield
If you need to work with C10/C8 tails, then just set up a different lipid type in CHARMM-GUI - there is a menu where you choose lipid types and quantities. If you ask for DOPC, you will get DOPC, and tinkering with the topology without understanding how it works will eventually cause trouble.
Sir, in the membrane builder I didn’t see the menu for options tails size C10C8 … Couldn’t include less than C18C18. …I have checked all … one by one
Ok, then there’s a different question to ask - how to set up a C10/C8 bilayer system given that CHARMM-GUI doesn’t support such short lipids. It seems to support short ones down to C10 though:
but my guess is you need unsaturated ones, and even shorter? Are you sure such lipids form bilayers in the first place? I honestly don’t know what the shortest bilayer-forming unsaturated lipid is.
There might be valid ways to convert a short lipid into an even shorter one, but you’d have to explain the rationale/requirements in more detail, including what you mean by the “extra ester linkage”.
yes this is the problem my molecules is DOPC10C8 while glucoseC10C8… this glycose is also did not present so my question is that when I generated the structure for glucose contains extra ester bonds , also dopc carbon size is also did not present than I manually deleted the extra carbons from itp files and renumber their position accordingly to my pdb bilayers that’s the problem… now when I put gmx … show that errors
Wait, where does glucose come into this? Seems you’re trying to build some very custom lipid that doesn’t exist in any force field. Please explain from the very beginning what the exact composition of the head and the tails is, including degrees of saturation of the lipids, numbering of ester linkages, whether or not it contains glycerol etc.
Actually sir I am doing the MD simulation of phospholipid and glycolipids… The fraction of glycolipids is glucoseC10c8… While phospholipid is fraction is dopc C10… Than I try to build the charmm GUI files for gromacs…both molecules are not available… Exactly position like glycolipids molecules contains some ester linkage while also have a problem of extra tail size and phospholipid molecules exactly is not available… Now I have generated the files but contains some extra Carbon linkage … because dopc is available in charmm GUI which start from C18/C18 …and ester linkage present in glucose in the tails position … Now I want to modified both these ITP files accordingly to my bilayer…than what to do next ?
I don’t understand what you mean by “[my] phospholipid fraction is DOPC C10”. DOPC is C18/C18, and is omega-9 unsaturated.
Where do these components come from, an experimental setup? If you absolutely need to use a glycolipid with glucose head, then you should prepare it with Glycan Builder. It again can generate shortest diacylglyceroles of 12 carbons, but that’s easier to work with than 18, and you can add your ester linkages as you desire. Then in principle you could edit your topology (not by hand, I’d recommend Gromologist routines for removing atoms to keep the topology consistent) to remove the few extra carbons, convert the terminal carbon to a hydrogen, and only then perhaps use Packmol to prepare the bilayer structure. I’d say you don’t want to go through gmx pdb2gmx, just adjust and recycle the topology files you get from CHARMM-GUI.
(There’s also the question of whether your tails are saturated or not, let’s not forget about it.)
But the question is, do you actually need such a non-standard setup, or can your scientific question be answered by the means of bilayer components available in CHARMM-GUI. This is not a simple workflow, and there are many points at which something can go wrong if you’re not experienced in working with these tools.
Let me explain you sir again in details
I am doing the MD simulation of membrane containing phospholipid and glycolipids… My molecules for phospholipid is DOPC contains tails size C10C8 … tails are saturated. symmetrical…
While another molecules is glycolipids head containg glycerol while tails size is C10C8 also saturated… Now the question is that when I use charmm GUI these structures are exactly not available. Because in membrane builder docp is C18/C18 while in the glycan builder structure containg some extra Carbon and ester linkage … Now I create the topology of these both in charmm GUI. It’s generated the output of docp C18/18 while for glycolipids C12C12 but I can’t proceeds with energy minimization because it will need to adjust accordingly my requirements…now the question is that I will need the size of C10C8 than how to remove these extra Carbon from tail size and how to remove these ester linkage from diacylglycerol? How to edit topology ? To fit Accordingly my requirements… Because I need topology containing Dop C10C8 while glycolipids C10C8 tails size…
