Applying pdb2gmx on a normal pdb file doesn't work with CHARMMS force field

User discussions
1

GROMACS version: 2022.03
GROMACS modification: Yes/No
Here post your question

Dear users.

My .pdb file is a normal file which was generated by ambertools. I also cross-tested this problem with KALP.pdb files of the tutorial. Both files resulted a fatal error when I use the command:

gmx pdb2gmx -f 'filename'.pdb -o 'filename'_processed.gro -ignh -ter -water spc

and choose

8 CHARMM27 all-atom force field

.

The error message is:

Fatal error:
Residue type 'NH2' not found in residue topology database

(The default label of N-terminal amide atoms of ambertools, NHE, also causes same error)

It’s my first time using CHARMM27, and I don’t know much about precautions.
I have tried to find the reason and hint of this problem but I cannot have found a user who confronts similar problem.

May I borrow your advice?

Thanks for your time and attention!

(fixed at 27 Jan) I read Protein-Ligand Complex and make hypothesis that by replacing NH2 to JZ4, pdb2gmx could be worked.

Actually, it allows me to step to select start terminus type. But there are 4 options (0: NH3+ / 1: NH2 / 2: 5’ / 3: None) instead 3 options. Is it right?

<<>>
8

Using the Charmm27 force field in directory charmm27.ff

going to rename charmm27.ff/aminoacids.r2b
Opening force field file /usr/local/gromacs/share/gromacs/top/charmm27.ff/aminoacids.r2b

going to rename charmm27.ff/rna.r2b
Opening force field file /usr/local/gromacs/share/gromacs/top/charmm27.ff/rna.r2b
Reading KALP-15_princ.pdb...
Read 'frame t= 1.000', 109 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 17 residues with 109 atoms

  chain  #res #atoms

  1 ' '    17    109

All occupancies are one
All occupancies are one
Opening force field file /usr/local/gromacs/share/gromacs/top/charmm27.ff/atomtypes.atp

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

Back Off! I just backed up topol.top to ./#topol.top.3#

Processing chain 1 (109 atoms, 17 residues)	

Identified residue ACE1 as a starting terminus.

Identified residue NH217 as a ending terminus.

-------------------------------------------------------
Program:     gmx pdb2gmx, version 2022.3
Source file: src/gromacs/gmxpreprocess/resall.cpp (line 645)

Fatal error:
Residue type 'NH2' not found in residue topology database

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

An amide capping group can be built onto the C-terminus using the CT2 terminal patch in aminoacids.c.tdb (you must choose this interactively when prompted by pdb2gmx) and does not require a special “NH2” residue.

3

Thanks for the advice!
But Sorry, after several trials, I admitted that I cannot fully understand your advice.
I can understand that the name which should be inserted behind the amide cap(or C-terminal atom or ‘???’) is not ‘NH2’. But what should I name it?

(KALP-15_princ.pdb file)
ATOM    202  N   ???     10      30.955  19.193  -0.000  1.00  0.00
ATOM    203  HN1 ???     10      30.479  20.084   0.000  1.00  0.00
ATOM    204  HN2 ???    10      31.964  19.159  -0.000  1.00  0.00

I have tried several candidates in ??? location (ex: CT2, JZ4, NHE etc…)
But after I selected CT2 as the end terminus type, all trials resulted as a fatal error. For example (when I insert CH2 in ??? location),

Fatal error:
Residue 'CT2' not found in residue topology database

I read pdb2gmx manual page but cannot find an answer for this.
May I be allowed more advice about the name of ‘???’?

Sincerely.

4

The residue name is the same as whatever the terminal residue is. Or just leave these atoms off entirely and choose the CT2 terminus patch and have pdb2gmx build them for you.

5

Thanks for the advice despite my continuous question…

Could I understand your advice as ‘I can use the law KALP-15 file (‘entirely leave these atoms off’)’
or ‘I can rename the 3 residues at the end lines to terminal residue (‘residue name is the same as whatever the terminal residue’) (ALA, in the case of KALP-15)’?

But the law KALP-15 file results fatal error

Fatal error:
Residue type 'NH2' not found in residue topology database

And rename to ALA (NH2 to ALA) resulted

Fatal error:
Atom CA in residue ACE 1 was not found in rtp entry ACE with 6 atoms
while sorting atoms.

ps. I also tried to rename to NME after I read
https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2012-June/072268.html
but the same error occurred

Fatal error:
Residue type 'NME' not found in residue topology database

What did I misunderstand in your advice?

Sincerely.

6

Sometimes terminal patches can build on the requisite atoms. In that case, e.g. NH2 at the C-terminus, you don’t need anything other than the terminal amino acid and to choose CT2 as the C-terminal patch when prompted by pdb2gmx. You will get a resulting structure that has ALA as the residue name for all atoms in the last residue, but with the constituent atoms of the CT2 patch as part of it.

7

Thanks for advice. Finally it worked well!