Why did I get an error related to the terminal caps?

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1

GROMACS version: gmx pdb2gmx, version 2021.3
GROMACS modification: No

Purpose: To cap both termini of a protein by ACE and NME and make the topology file.
My attempt:

  1. To add ACE and NME by PyMOL and NME is renamed to CT1.
  2. gmx pdb2gmx -ff charmm27 -f protein_test.pdb -water tip3p

I tried to make the topology file via gmx pdb2gmx command, but I failed and got the following error.
Could you please help me to resolve this issue?

$ bash test.sh
                     :-) GROMACS - gmx pdb2gmx, 2021.3 (-:

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GROMACS:      gmx pdb2gmx, version 2021.3
Executable:   /Users/me/.local/gromacs-2021.3/build/bin/gmx
Data prefix:  /Users/me/.local/gromacs-2021.3 (source tree)
Working dir:  /Users/me/Dropbox/00_Research/16_koff_estimation/data/02_prep_system/thrombin/1bmn/test
Command line:
  gmx pdb2gmx -f protein_test.pdb -ff charmm27 -water tip3p

Using the Charmm27 force field in directory charmm27.ff

going to rename charmm27.ff/aminoacids.r2b
Opening force field file /Users/me/.local/gromacs-2021.3/share/top/charmm27.ff/aminoacids.r2b

going to rename charmm27.ff/rna.r2b
Opening force field file /Users/me/.local/gromacs-2021.3/share/top/charmm27.ff/rna.r2b
Reading protein_test.pdb...
Read '', 91 atoms

Analyzing pdb file
Splitting chemical chains based on TER records or chain id changing.

There are 1 chains and 0 blocks of water and 11 residues with 91 atoms

  chain  #res #atoms

  1 'I'    11     91

All occupancies are one
All occupancies are one
Opening force field file /Users/me/.local/gromacs-2021.3/share/top/charmm27.ff/atomtypes.atp

Reading residue database... (Charmm27)
Opening force field file /Users/me/.local/gromacs-2021.3/share/top/charmm27.ff/aminoacids.rtp
Opening force field file /Users/me/.local/gromacs-2021.3/share/top/charmm27.ff/dna.rtp
Opening force field file /Users/me/.local/gromacs-2021.3/share/top/charmm27.ff/lipids.rtp
Opening force field file /Users/me/.local/gromacs-2021.3/share/top/charmm27.ff/rna.rtp
Opening force field file /Users/me/.local/gromacs-2021.3/share/top/charmm27.ff/aminoacids.hdb
Opening force field file /Users/me/.local/gromacs-2021.3/share/top/charmm27.ff/dna.hdb
Opening force field file /Users/me/.local/gromacs-2021.3/share/top/charmm27.ff/lipids.hdb
Opening force field file /Users/me/.local/gromacs-2021.3/share/top/charmm27.ff/rna.hdb
Opening force field file /Users/me/.local/gromacs-2021.3/share/top/charmm27.ff/aminoacids.n.tdb
Opening force field file /Users/me/.local/gromacs-2021.3/share/top/charmm27.ff/dna.n.tdb
Opening force field file /Users/me/.local/gromacs-2021.3/share/top/charmm27.ff/rna.n.tdb
Opening force field file /Users/me/.local/gromacs-2021.3/share/top/charmm27.ff/aminoacids.c.tdb
Opening force field file /Users/me/.local/gromacs-2021.3/share/top/charmm27.ff/dna.c.tdb
Opening force field file /Users/me/.local/gromacs-2021.3/share/top/charmm27.ff/rna.c.tdb

Processing chain 1 'I' (91 atoms, 11 residues)

Identified residue ACE55 as a starting terminus.

Identified residue CT364 as a ending terminus.
8 out of 8 lines of specbond.dat converted successfully
Start terminus ACE-55: NH3+
End terminus CT3-64: CT3

-------------------------------------------------------
Program:     gmx pdb2gmx, version 2021.3
Source file: src/gromacs/gmxpreprocess/pdb2top.cpp (line 1104)

Fatal error:
atom N not found in buiding block 1ACE while combining tdb and rtp

For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------
2

What are you trying to build? The error says There is a mismatching or missing atoms from your input pdb with that of files in ff. Also, did you tried with -ter flag?

1 Like
3

ACE and NME cap require an empty terminus (“None”). The default behavior of pdb2gmx is to try to add NH3+ and COO- terminus as for a normal peptide. As suggested, use the -ter command line flag and select None for terminus at both end.

1 Like
4

ACE and NME cap require an empty terminus (“None”). The default behavior of pdb2gmx is to try to add NH3+ and COO- terminus as for a normal peptide. As suggested, use the -ter command line flag and select None for terminus at both end.

Thank you. I have resolved the issue.
I did not know how -ter None works. After using -ter flag and selecting None, I succeed in getting a structure whose termini are capped by aceyl and nmetyl groups :)