No default bondtype, U-B type etc. detected by grompp for nonstandard residue, GLYM

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1

GROMACS version:2019.4
GROMACS modification: No
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I have a protein with a nonstandard residue GLYM. I am using CHARMM36-2019 where it is included in .rtp file. When I am doing pdb2gmx I am getting error like:

Fatal error:
The residues in the chain GLYM2–GLN500 do not have a consistent type. The
first residue has type ‘Other’, while residue ALA3 is of type ‘Protein’. 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.

Now, I cannot change chainId because then it will be treated as different molecule when I’ll do grompp I’ll get many errors like :

ERROR 1 [file topol.top, line 150573]:
No default Bond types

In these bonds one atoms are from GLYM like C of GLYM and N of next residue ALA.

Can I define GLYM as “protein”, not as “others”?? How to modify that??

Could you please help me to solve this??

Thanks, in advance.

With regards,
Puja

2

Hi,

You can check the definition of the residues GLYM in rtp file. The link (bond) between GLYM and the neighboring residues is properly defined.
For example the entry 'C +N ’ under [bonds] maybe is missing in rtp file for the [GLYM].

Best regards
Alessandra

3

Thanks Alevilla. That is solved. As GLYM was not included in residuetypes.dat it was not treated as protein chain and there was no bond with the next residue.

Now, the issue is I am not able to build the topology file with pdb2gmx when I am having GLYM as residue 1 of protein chain.

I am getting the error

Fatal error:
Residue 1 named GLYM of a molecule in the input file was mapped
to an entry in the topology database, but the atom HN used in
an interaction of type improper in that entry is not found in the
input file. Perhaps your atom and/or residue naming needs to be
fixed.

So, it is clearly the issue with N terminal atoms. I found there is no entry for GLYM in merged.n.tbd file that makes changes to the n-terminal residue. Like for GLY the entry is

; CHARMM NGNE patch, new
[ GLY-NH2 ]
[ replace ]
N NH2 14.007 -0.96
CA CT2 12.011 0.10
HA1 HB2 1.008 0.09
HA2 HB2 1.008 0.09
[ add ]
2 4 H N CA C
H 1.008 0.34 -1
[ delete ]
HN

I have GLYM, When I am adding the option -v to pdb2gmx, it is showing

Deleting atom ‘HN’ in residue ‘GLYM’ 2

and then it is showing the error

Fatal error:
Residue 1 named GLYM of a molecule in the input file was mapped
to an entry in the topology database, but the atom HN used in
an interaction of type improper in that entry is not found in the
input file. Perhaps your atom and/or residue naming needs to be
fixed.

For GLYM no n-terminal modification is needed. How to do that?

With regards,
Puja

4

Choose ‘None’ as the N-terminus type.

5

Thanks, Justin. Where should I do that?

Puja

6

When prompted to choose termini by pdb2gmx.

7

Thank you so much, Justin. It worked exactly how I wanted.

Puja