I designed a 12 residue peptide FP(G)9K with pymol and made it protonated and neutral. Then saved this molecule as a pdb. When I was running the pdb to gmx command in gromacs, I got an error message " atom 001 in residue lys 13 was not found in rtp entry clys with 23 atoms while sorting atom " It does not matter whether it is a protonated or neutral lys.
As I looking for gromacs mannul it says "If you are attempting to assemble a topology using pdb2gmx, the atom names are expected to match those found in the .rtp file that define the building block(s) in your structure. In most cases, the problem arises from a naming mismatch, so simply re-name the atoms in your coordinate file appropriately. In other cases, you may be supplying a structure that has residues that do not conform to the expectations of the force field, in which case you should investigate why such a difference is occurring and make a decision based on what you find - use a different force field, manually edit the structure, etc."
I wonder what should I change in the pdb file to make it right? Thank you!
Dear Zhichao Zhang,
You should check the atom names and residue names of your PDB file. Both fields must match the ones found in the "aminoacids.rtp" file for the provided forcefield.
Best,
Felippe
This question was eventually answered in detail on the Quora Forum:
https://www.quora.com/How-can-I-complete-a-missing-atom-in-a-protein-I-am-unable-to-do-the-pdb2gmx-can-someone-please-assist-me-to-complete-the-missing-atom-in-this-protein-4MGP-pdb-you-can-download-the-protein-from-the-link-given-below
Hi Zhichao! First of all, and this is the most important thing, you shall find out what protonation states will your aminoacids have at the pH which you are going to use during your simulations. You can check them in the litterature. Second is that you need check out the rtp-file from the force field and see if aminoacids can be found at that protonation state. Consider where those aminoacids are situated in the chain/sequence. Then you can proceed further by editing the structure until it will match the structures from the database.
You have mentioned that you have designed the peptide by yourself. As I understand you have used the molecular graphics software. It means that highly likely the order in your own file won't match the structures which are in the database: it can happen that carbons might have a different names and there might be the wrong number of protons as well. I could advice you to use Avogadro in order to get your peptide right or to get the structure from the pdb-databank. Then the only problem you might face is protons. Moreover, if the total charge of your peptide won't be equal to zero you shall add some ions in the simulation box to compensate it.
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