GROMACS version:2020.1
GROMACS modification: No
Dear friends,
I want to run a simulation of DPC micelle with 65 molecules and a peptide within it. Like DPPC and KALP tutorial i tried to do it. I made a topology for pure DPC as I learnt from the tutorial :
That is actually very simple. As the error is self-explaining, you have 20410 coordinates in your coordinate file (pdb), while you have specified 22880 ones in the topology. This means that either your topology includes more atoms, or your structure file includes less than expected.
thanks for your attention. I downloaded my pdb file from here as it shows, it has 65 DPC molecules and 6305 water molecules. Then I wrote my topol-dpc.topology as I wrote it above in the topic, I think something else is wrong.
here is pdb of my main structure, and this is pdb of peptide within the structure. topol.top (44.1 KB) topol-dpc.top (498 Bytes) minim (copy).mdp (173 Bytes)
again thank you for your help.
You haven’t included the dpc.itp file, which is important for determining any possible differences. You don’t need to do this minimization though; that’s somewhat unique to the tutorial, which starts from “broken” bilayer coordinates. Your micelle isn’t broken across periodic boundaries.
Then here is the problem. The PDB file of your m65 does not contain all the dpc atoms in one residue. You have 65 dpc molecules which equals 3965 atoms (61 atoms each). While you only have 23 atoms in each DPC residue embedded in the m65.pdb. The difference is 2470 atoms which is what GROMACS is complaining about.
Dear Ali
As you told me, I used Avogadro to add Hydrogen atoms to DPC molecules but received this error.
Do you know any other software or other way to solve this? This is my new pdb file.
Well from the first look, it seems to me that you have added 53 extra atoms somewhere. Just compare the first residue in your dpcmicelle.pdb with the atoms in the dpc.itp. What you want to look is differences between the residues in the micelle and the .itp file.
The new pdb file you added still has problems. have a look at this to understand more about the pdb format if you haven’t already (https://zhanglab.ccmb.med.umich.edu/SSIPe/pdb_atom_format.html)
check the residue number 1 in the micelle for instance, there is only 23 atoms in it. while it should contain 61 atoms. I don’t know where you have added the hydrogens but both the old and new micelle files look still the same.
In other words, you must have the same atoms in lines 64-124 of the dpc.itp, for all the residues in dpcmicelle.pdb. but only checking the first residue (rows 3-25) of the dpcmicelle.pdb says that your system lacks some atoms.
