Problem with chain definition, still trying to add NAG to forcefield so I can run simulations

User discussions
1

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GROMACS modification: Yes/No
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I have been trying to add NAG to forcefield Gromos54a7:
Fatal error:
Residue ‘NAG’ not found in residue topology database

I have generated a forcefield.itp and topology for NAG through CHARMM-GUI.
I have added NAG to the aminoacids.itp
I have #include “toppar/forcefield.itp” in the Gromos54a7 forcefield.itp file

Warning:
Warning: No residues in chain starting at NAG1 identified as Protein/RNA/DNA.
This makes it impossible to link them into a molecule, which could either be
correct or a catastrophic error. Please check your structure, and add all
necessary residue names to residuetypes.dat if this was not correct.

I have located the residuetype.dat and tried adding NAG as Protein, atom, etc., anything really to try and get it to work.

Fatal error:
The residues in the chain NAG1–FUC9 do not have a consistent type. The first
residue has type ‘Atom’, while residue BMA3 is of type ‘Other’. Either there
is a mistake in your chain, or it includes nonstandard residue names that have
not yet been added to the residuetypes.dat file in the GROMACS library
directory. If there are other molecules such as ligands, they should not have
the same chain ID as the adjacent protein chain since it’s a separate
molecule.

So I have changed NAG to other in the residuetype.dat, and then it reverts back to the original:

Warning: No residues in chain starting at NAG1 identified as Protein/RNA/DNA.
This makes it impossible to link them into a molecule, which could either be
correct or a catastrophic error. Please check your structure, and add all
necessary residue names to residuetypes.dat if this was not correct.

Warning: No residues in chain starting at NAG2 identified as Protein/RNA/DNA.
This makes it impossible to link them into a molecule, which could either be
correct or a catastrophic error. Please check your structure, and add all
necessary residue names to residuetypes.dat if this was not correct.

Warning: No residues in chain starting at NAG5 identified as Protein/RNA/DNA.
This makes it impossible to link them into a molecule, which could either be
correct or a catastrophic error. Please check your structure, and add all
necessary residue names to residuetypes.dat if this was not correct.

Warning: No residues in chain starting at NAG8 identified as Protein/RNA/DNA.
This makes it impossible to link them into a molecule, which could either be
correct or a catastrophic error. Please check your structure, and add all
necessary residue names to residuetypes.dat if this was not correct.

Problem with chain definition, or missing terminal residues.
This chain does not appear to contain a recognized chain molecule.
If this is incorrect, you can edit residuetypes.dat to modify the behavior.
8 out of 8 lines of specbond.dat converted successfully

Program: gmx pdb2gmx, version 2020.1-Ubuntu-2020.1-1
Source file: src/gromacs/gmxpreprocess/resall.cpp (line 557)

Fatal error:
Residue ‘NAG’ not found in residue topology database

How do I correct this? I am a beginner and I am getting frustrated. I don’t understand. Also I am using Gromacs through Ubuntu (version 2020.1-Ubuntu-2020.1-1) as I have a windows computer if that means anything.

2

Hi,
A question (since I do not know): do you know if CHARMM-GUI generates topology for GROMOS54a7 force field?
If no, it is better to avoid to mix force field.
Thank you
Alessandra

3

Hello,
I just checked, it is only showing Charmm36m, Charmm36, opsala, and amber. So, because you brought up this point. I have actually added the Charmm36 (most recent 2022) force field to my directory. Now, in that file there is a carb.rtp. Should I add my generated carb.itp atoms and bonds for NAG to this file? Also should I add the generated forcefield.itp also to this Charmm36 file? And when I add to the residuetype.dat file would NAG be considered a Carb type?

Thanks,
Heather

4

You cannot directly add .itp contents to an .rtp file, but you can use the information to construct a suitable residue definition.

Based on the notes above, if you have a polysaccharide chain, it’s not necessary to define it at all. As long as every residue in a chain has the same residue type (which can include “Other”), then you don’t need to do anything. You do need to define a residue type for e.g. a modified amino acid so that it is recognized as Protein and therefore contiguous with the polypeptide chain.

5

ok, so when I was going through the carb.rtp from CHARMM36. I realized that the BGLCNA is my NAG. So I copied and pasted the same coordinates and renamed it NAG so the PDB can be read. Now I am getting:

WARNING: atom H1 is missing in residue NAG 2 in the pdb file
You might need to add atom H1 to the hydrogen database of building block NAG
in the file carb.hdb (see the manual)

WARNING: atom O1 is missing in residue NAG 2 in the pdb file

WARNING: atom HO1 is missing in residue NAG 2 in the pdb file
You might need to add atom HO1 to the hydrogen database of building block NAG
in the file carb.hdb (see the manual)

WARNING: atom H5 is missing in residue NAG 2 in the pdb file
You might need to add atom H5 to the hydrogen database of building block NAG
in the file carb.hdb (see the manual)

WARNING: atom H2 is missing in residue NAG 2 in the pdb file
You might need to add atom H2 to the hydrogen database of building block NAG
in the file carb.hdb (see the manual)

WARNING: atom HN2 is missing in residue NAG 2 in the pdb file
You might need to add atom HN2 to the hydrogen database of building block NAG
in the file carb.hdb (see the manual)

WARNING: atom H81 is missing in residue NAG 2 in the pdb file
You might need to add atom H81 to the hydrogen database of building block NAG
in the file carb.hdb (see the manual)

WARNING: atom H82 is missing in residue NAG 2 in the pdb file
You might need to add atom H82 to the hydrogen database of building block NAG
in the file carb.hdb (see the manual)

WARNING: atom H83 is missing in residue NAG 2 in the pdb file
You might need to add atom H83 to the hydrogen database of building block NAG
in the file carb.hdb (see the manual)

WARNING: atom H3 is missing in residue NAG 2 in the pdb file
You might need to add atom H3 to the hydrogen database of building block NAG
in the file carb.hdb (see the manual)

WARNING: atom HO3 is missing in residue NAG 2 in the pdb file
You might need to add atom HO3 to the hydrogen database of building block NAG
in the file carb.hdb (see the manual)

WARNING: atom H4 is missing in residue NAG 2 in the pdb file
You might need to add atom H4 to the hydrogen database of building block NAG
in the file carb.hdb (see the manual)

WARNING: atom HO4 is missing in residue NAG 2 in the pdb file
You might need to add atom HO4 to the hydrogen database of building block NAG
in the file carb.hdb (see the manual)

WARNING: atom H61 is missing in residue NAG 2 in the pdb file
You might need to add atom H61 to the hydrogen database of building block NAG
in the file carb.hdb (see the manual)

WARNING: atom H62 is missing in residue NAG 2 in the pdb file
You might need to add atom H62 to the hydrogen database of building block NAG
in the file carb.hdb (see the manual)

WARNING: atom HO6 is missing in residue NAG 2 in the pdb file
You might need to add atom HO6 to the hydrogen database of building block NAG
in the file carb.hdb (see the manual)

Is there a way to generate a .hdb? I tried to find BGLCNA in the carb.hdb but I did not find anything. Also, I am confused about the atoms not being in the PDB file, because when I look in the PDBeditor they are all there minus the O1, which I need to add.

6

It’s there in the latest (July 2022) version of carb.hdb:

BGLCNA     12
1       5       H1      C1      C2      O1      O5
1       2       HO1     O1      C1      C2
1       5       H5      C5      C4      C6      O5
1       5       H2      C2      C1      C3      N
1       1       HN      N       C       C2
3       4       HT      CT      C       N
1       5       H3      C3      C2      C4      O3
1       2       HO3     O3      C3      C2
1       5       H4      C4      C3      C5      O4
1       2       HO4     O4      C4      C3
2       6       H6      C6      C5      O6
1       2       HO6     O6      C6      C5

Check all the nomenclature because atoms like H8[123] are not standard atom names for BGLCNA (maybe what you’re calling H8[123] should be HT[123] according to the residue definition).

7

Hello,

I hope you are well. I figured out the .hdb and yes all of them were there. I added all my carb names to match the PDB file names, and then corrected my atoms in the PDB file (i.e. C8 to CT, etc.) Now when I run it I get this:

Processing chain 5 ‘E’ (89 atoms, 7 residues)
Identified residue NEG1 as a starting terminus.
Identified residue NAG8 as a ending terminus.
8 out of 8 lines of specbond.dat converted successfully
Start terminus NEG-1: NH3+
End terminus NAG-8: COO-
Opening force field file /usr/share/gromacs/top/charmm36.ff/aminoacids.arn
Checking for duplicate atoms…
Generating any missing hydrogen atoms and/or adding termini.
Segmentation fault (core dumped)

I read in some other posts that this may be a bug? Or do I need to do something to resolve it?

Thanks in advance,
Heather