Residue 1 named LYS of a molecule in the input file was mapped
to an entry in the topology database, but the atom CB used in
that entry is not found in the input file. Perhaps your atom
and/or residue naming needs to be fixed.
Can anyone tell me what is this error means?
my pdb contain CB under LYS 1 Residue !
how to fix this problem?
Thanks
The issue is with pdb2gmx, so it is nothing to do with .itp files or .mdp settings.
You have a missing atom. If you think it's there and pdb2gmx says it's not, then either (1) the format of the PDB file is wrong such that its contents are uninterpretable or (2) you're not looking at the right atom. Note that pdb2gmx uses its own internal numbering, and if you have multiple chains or missing residues, it may be referring to a different residue. If the PDB file comes from the RCSB, look for "MISSING" lines in the header.
The issue is with pdb2gmx, so it is nothing to do with .itp files or .mdp settings.
You have a missing atom. If you think it's there and pdb2gmx says it's not, then either (1) the format of the PDB file is wrong such that its contents are uninterpretable or (2) you're not looking at the right atom. Note that pdb2gmx uses its own internal numbering, and if you have multiple chains or missing residues, it may be referring to a different residue. If the PDB file comes from the RCSB, look for "MISSING" lines in the header.
Hi,
I am a beginner in GROMACS. If the atom is listed in the "MISSING" lines in the header, what is to be done in that case?
If you are missing terminal residues that are not likely relevant for dynamics, you don't have to do anything necessarily. If you are missing atoms from the constituent residues, you have to model them back using other software before trying to run anything with GROMACS.
So how make an .itp file for capped amino acid? It is not possible with pdb2gmx?
pdb2gmx can do anything the force field can do. If your chosen force field supports a single amino acid and capping groups (I'm assuming acetyl and amide), then pdb2gmx can do that.
Thank you, I mean AMBER99 and yes acetyl and amide. Can AMBER99 do that in gromacs?
Possibly. ACE and NME residues exist as capping groups, but must be named as such in the input PDB. I suggest you seek specific technical advice via gmx-users if you need it.
I think the challenge in .itp file are charges. Is it possible to calculate charges for example by DFT and read atomtypes from gromacs top/amber99ff directory, so make .itp file yourself. Is it true?
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