Capping residue ACE not recognised from the rtp file

User discussions
,
1

GROMACS version:5.1.4
GROMACS modification: No
After capping my protein with ACE[acetyl group] using pymol build tool, i couldnt continue after pdb2gmx because of the following error:

Residue 2 named ACE of a molecule in the input file was mapped to an entry in the topology database, but the atom C used in that entry is not found in the input file. Perhaps your atom and/or residue naming needs to be fixed

For your info:

  1. the ff used is CHARMM36M
  2. i did rename the atoms according to the force field rtp file [merged.rtp]
    rtp
    rtp757×332 30 KB

    3.This is my pdb file after capping using pymol
    pdb
    pdb1777×418 93.9 KB

How do i tackle this issue?
I tried a similar case from Prof Lemkul’s umbrella sampling tutorials where the N terminal is capped with ACE[ff–>GROMOS9653a6], i get a similar warning for ALA terminus. but it’s just a warning not an error.

thanks!

2

I couldn’t solve this without ignoring hydrogens, there were a couple of answers given years back…

Capping of peptide terminal ends

!!

3

The original issue points to pdb2gmx thinking that ACE is your terminal residue and it is trying to apply the COO- patch, but fails to find atom C. Ignoring H shouldn’t be linked to this issue. When reporting problems with pdb2gmx, please always include the entire screen output. There are critical bits of information that you may think are irrelevant that are key to solving these issues.

4

Sure professor…I will follow your advice…Details are critical…
Now with regard to the input i have added the -ter flag and chose None for the ACE cap.
the output from pdb2gmx;

yes!! i have been roaming around this issue editing my pdb…Now it makes sense!!

image
image1816×904 131 KB

and yes… i learnt that this isn’t correlated.

Thank you, sir.

5

Are you still having an issue, or is it solved? The screenshot is not helpful as it omits all of the important upstream information. If you need further help working this out, please simply copy and paste the entire terminal output from pdb2gmx.

6

Sorry about the delay due to the site being down…

The output of the pdb2gmx file is down…

Using the Charmm36-feb2021 force field in directory ./charmm36-feb2021.ff

Opening force field file ./charmm36-feb2021.ff/merged.r2b
Reading capped.pdb…
Read 548 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 75 residues with 548 atoms

  • chain #res #atoms*
  • 1 ‘A’ 75 548 *

All occupancies are one
Opening force field file ./charmm36-feb2021.ff/atomtypes.atp
Atomtype 448
Reading residue database… (charmm36-feb2021)
Opening force field file ./charmm36-feb2021.ff/merged.rtp
Residue 1248
Sorting it all out…
Opening force field file ./charmm36-feb2021.ff/merged.hdb
Opening force field file ./charmm36-feb2021.ff/merged.n.tdb
Opening force field file ./charmm36-feb2021.ff/merged.c.tdb

Back Off! I just backed up topol.top to ./#topol.top.2#
Processing chain 1 ‘A’ (548 atoms, 75 residues)
Analysing hydrogen-bonding network for automated assignment of histidine

  • protonation. 112 donors and 104 acceptors were found.*
    There are 147 hydrogen bonds
    Will use HISE for residue 329
    Will use HISE for residue 330
    Will use HISE for residue 362
    Will use HISE for residue 374
    Identified residue ACE305 as a starting terminus.
    Identified residue NME379 as a ending terminus.
    8 out of 8 lines of specbond.dat converted successfully
    Special Atom Distance matrix: 
  •              CYS322  HIS329  HIS330  HIS362*

  •               SG130  NE2178  NE2188  NE2434*
  • HIS329 NE2178 1.594*
  • HIS330 NE2188 2.003 1.245*
  • HIS362 NE2434 1.550 1.963 1.335*
  • HIS374 NE2520 3.024 4.258 3.736 2.503*
    Select start terminus type for ACE-305
  • 0: NH3+*
  • 1: NH2*
  • 2: 5TER*
  • 3: None*
    3
    Start terminus ACE-305: None
    Select end terminus type for NME-379
  • 0: COO-*
  • 1: COOH*
  • 2: CT2*
  • 3: 3TER*
  • 4: None*
    4
    End terminus NME-379: None
    Opening force field file ./charmm36-feb2021.ff/merged.arn
    Checking for duplicate atoms…
    Generating any missing hydrogen atoms and/or adding termini.

-------------------------------------------------------
Program gmx pdb2gmx, VERSION 5.1.4
Source code file: /home/allwin/Downloads/gromacs-5.1.4/src/gromacs/gmxpreprocess/pgutil.c, line: 147

Fatal error:
Residue 2 named ACE of a molecule in the input file was mapped
to an entry in the topology database, but the atom C used in
that entry is not found in the input file. Perhaps your atom
and/or residue naming needs to be fixed.

For more information and tips for troubleshooting, please check the GROMACS
website at Errors - Gromacs
-------------------------------------------------------

A follow up question with regard to pdb2gmx
1. Hydrogens are causing trouble because of the different nomenclature in the pdb and the rtp files [HB3<–>HB2; Missing atoms while sorting]
Is there any way to overcome this issue without replacing the atom names in the pdb file?

2. how much will the -ignh flag affect the results; Will hydrogens be neglected prior to that step? the hydrogens are just not removed i suppose. they are ignored;; and the energy minimization step still has the max force on hydrogens, That’s the reason i had this question.

Thank you!

7

The fact that pdb2gmx is calling this residue 2 and not 1 suggests you perhaps have an issue in the coordinate file (e.g. duplicate ACE entries) because there should not be any atom named C in the ACE residue in the CHARMM force field.

No, atom names must match the force field’s expectations.

-ignh does not mean hydrogens are removed from the structure, only that pdb2gmx ignores the ones you provide and generates its own set of new H atoms, appropriately named, and constructed with ideal geometries.

8

In response to this suggestion, i checked the pdb file and found no other ACEs.

In order to focus on the problem, i made a simple dipeptide ValAla and capped both ends using Pymol 1.8.4.0. [Acetyl in N and N-Meth in C]
the pdb file is below::
The residues in the caps have been named according to the charmm36ff [merged.rtp file]
ATOM 1 CY ACE 0 -1.812 -1.102 -1.417 1.00 0.00 C
ATOM 2 OY ACE 0 -2.005 -0.026 -1.999 1.00 0.00 O
ATOM 3 CAY ACE 0 -2.725 -2.287 -1.644 1.00 0.00 C
ATOM 4 HY1 ACE 0 -2.715 -2.568 -2.687 1.00 0.00 H
ATOM 5 HY2 ACE 0 -2.395 -3.128 -1.052 1.00 0.00 H
ATOM 6 HY3 ACE 0 -3.736 -2.034 -1.360 1.00 0.00 H
ATOM 7 N ALA 1 -0.677 -1.230 -0.491 1.00 0.00 N
ATOM 8 CA ALA 1 -0.001 0.064 -0.491 1.00 0.00 C
ATOM 9 C ALA 1 1.499 -0.110 -0.491 1.00 0.00 C
ATOM 10 O ALA 1 2.030 -1.227 -0.502 1.00 0.00 O
ATOM 11 CB ALA 1 -0.509 0.856 0.727 1.00 0.00 C
ATOM 12 H ALA 1 -0.399 -2.106 0.076 1.00 0.00 H
ATOM 13 HA ALA 1 -0.269 0.603 -1.418 1.00 0.00 H
ATOM 14 1HB ALA 1 -1.605 1.006 0.691 1.00 0.00 H
ATOM 15 2HB ALA 1 -0.285 0.342 1.681 1.00 0.00 H
ATOM 16 3HB ALA 1 -0.053 1.861 0.784 1.00 0.00 H
ATOM 17 N VAL 2 2.355 1.085 -0.477 1.00 0.00 N
ATOM 18 CA VAL 2 2.695 1.361 -1.870 1.00 0.00 C
ATOM 19 C VAL 2 4.191 1.356 -2.072 1.00 0.00 C
ATOM 20 O VAL 2 4.962 1.929 -1.292 1.00 0.00 O
ATOM 21 CB VAL 2 2.073 2.746 -2.309 1.00 0.00 C
ATOM 22 CG1 VAL 2 2.494 3.279 -3.706 1.00 0.00 C
ATOM 23 CG2 VAL 2 0.525 2.764 -2.316 1.00 0.00 C
ATOM 24 H VAL 2 2.669 1.647 0.391 1.00 0.00 H
ATOM 25 HA VAL 2 2.280 0.557 -2.504 1.00 0.00 H
ATOM 26 HB VAL 2 2.406 3.504 -1.569 1.00 0.00 H
ATOM 27 1HG1 VAL 2 2.225 2.583 -4.524 1.00 0.00 H
ATOM 28 2HG1 VAL 2 2.029 4.256 -3.941 1.00 0.00 H
ATOM 29 3HG1 VAL 2 3.584 3.459 -3.779 1.00 0.00 H
ATOM 30 1HG2 VAL 2 0.106 2.463 -1.338 1.00 0.00 H
ATOM 31 2HG2 VAL 2 0.126 3.776 -2.520 1.00 0.00 H
ATOM 32 3HG2 VAL 2 0.100 2.083 -3.077 1.00 0.00 H
ATOM 33 NT NME 3 4.750 0.648 -3.233 1.00 0.00 N
ATOM 34 CAT NME 3 6.192 0.811 -3.170 1.00 0.00 C
ATOM 35 HNT NME 3 4.221 0.136 -3.953 1.00 0.00 H
ATOM 36 HT1 NME 3 6.439 1.699 -2.608 1.00 0.00 H
ATOM 37 HT2 NME 3 6.640 -0.045 -2.687 1.00 0.00 H
ATOM 38 HT3 NME 3 6.597 0.903 -4.167 1.00 0.00 H
END

____End of PDB file

the pdb file output for the peptide
Using the Charmm36-feb2021 force field in directory ./charmm36-feb2021.ff

Opening force field file ./charmm36-feb2021.ff/merged.r2b
Reading dipep.pdb…
Read 38 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 4 residues with 38 atoms

chain #res #atoms
1 ’ ’ 4 38

All occupancies are one
Opening force field file ./charmm36-feb2021.ff/atomtypes.atp
Atomtype 448
Reading residue database… (charmm36-feb2021)
Opening force field file ./charmm36-feb2021.ff/merged.rtp
Residue 1248
Sorting it all out…
Opening force field file ./charmm36-feb2021.ff/merged.hdb
Opening force field file ./charmm36-feb2021.ff/merged.n.tdb
Opening force field file ./charmm36-feb2021.ff/merged.c.tdb

Back Off! I just backed up topol.top to ./#topol.top.22#
Processing chain 1 (38 atoms, 4 residues)
Identified residue ACE0 as a starting terminus.
Identified residue NME3 as a ending terminus.
8 out of 8 lines of specbond.dat converted successfully
Select start terminus type for ACE-0
0: NH3+
1: NH2
2: 5TER
3: None
3
Start terminus ACE-0: None
Select end terminus type for NME-3
0: COO-
1: COOH
2: CT2
3: 3TER
4: None
4
End terminus NME-3: None
Opening force field file ./charmm36-feb2021.ff/merged.arn
Checking for duplicate atoms…
Generating any missing hydrogen atoms and/or adding termini.

Program gmx pdb2gmx, VERSION 5.1.4
Source code file: /home/sarcoma/gromacs-5.1.4/src/gromacs/gmxpreprocess/pgutil.c, line: 147

Fatal error:
Residue 2 named ACE of a molecule in the input file was mapped
to an entry in the topology database, but the atom C used in
that entry is not found in the input file. Perhaps your atom
and/or residue naming needs to be fixed.

For more information and tips for troubleshooting, please check the GROMACS
website at Common Errors — GROMACS webpage https://www.gromacs.org documentation

The same error shoots up as Residue 2 as ACE. But if the pdb file is raw from pymol and if i haven’t done the changes as in the rtp file then the error looks like this…

Fatal error:
Atom C in residue ACE 0 was not found in rtp entry ACE with 6 atoms
while sorting atoms.

Sir, would it be a problem in the residue database…? as the mapping part has some issue…

9

I confirm the issue exists also with GROMACS 2021.1. I created a simple glutamyl dipeptide (GLU_dipeptide.pdb) file in PyMOL:

ATOM     22  CAY ACE X   1      -0.410   0.146   0.154  1.00  0.00           C  
ATOM     23  CY  ACE X   1       1.048   0.238  -0.245  1.00  0.00           C  
ATOM     24  OY  ACE X   1       1.659  -0.755  -0.662  1.00  0.00           O  
ATOM     25 1HH3 ACE X   1      -0.529  -0.569   0.955  1.00  0.00           H  
ATOM     26 2HH3 ACE X   1      -0.762   1.110   0.490  1.00  0.00           H  
ATOM     27 3HH3 ACE X   1      -1.005  -0.170  -0.690  1.00  0.00           H  
ATOM      1  N   GLU X   2       1.662   1.368  -0.150  1.00  0.00           N  
ATOM      2  CA  GLU X   2       3.068   1.445  -0.537  1.00  0.00           C  
ATOM      3  C   GLU X   2       3.850   2.298   0.431  1.00  0.00           C  
ATOM      4  O   GLU X   2       3.426   3.390   0.835  1.00  0.00           O  
ATOM      5  CB  GLU X   2       3.184   2.014  -1.980  1.00  0.00           C  
ATOM      6  CG  GLU X   2       4.634   2.109  -2.557  1.00  0.00           C  
ATOM      7  CD  GLU X   2       4.823   2.713  -3.936  1.00  0.00           C  
ATOM      8  OE1 GLU X   2       3.846   3.103  -4.604  1.00  0.00           O  
ATOM      9  OE2 GLU X   2       5.999   2.807  -4.347  1.00  0.00           O1-
ATOM     10  H   GLU X   2       1.178   2.188   0.189  1.00  0.00           H  
ATOM     11  HA  GLU X   2       3.497   0.426  -0.516  1.00  0.00           H  
ATOM     12 2HB  GLU X   2       2.723   3.022  -2.023  1.00  0.00           H  
ATOM     13 3HB  GLU X   2       2.575   1.405  -2.677  1.00  0.00           H  
ATOM     14 2HG  GLU X   2       5.118   1.120  -2.584  1.00  0.00           H  
ATOM     15 3HG  GLU X   2       5.277   2.738  -1.920  1.00  0.00           H  
ATOM     16  NT  NME X   3       4.996   1.878   0.851  1.00  0.00           N  
ATOM     17  CAT NME X   3       5.767   2.682   1.783  1.00  0.00           C  
ATOM     18  H   NME X   3       5.356   0.990   0.531  1.00  0.00           H  
ATOM     19 1HH3 NME X   3       6.324   3.435   1.248  1.00  0.00           H  
ATOM     20 2HH3 NME X   3       5.106   3.169   2.486  1.00  0.00           H  
ATOM     21 3HH3 NME X   3       6.458   2.055   2.327  1.00  0.00           H  
END

and ran pdb2gmx as

gmx pdb2gmx -f GLU_dipeptide.pdb -ff charmm36-feb2021 -water tip3p -ter -ignh

The output after the header is:

Command line:
  gmx pdb2gmx -f GLU_dipeptide.pdb -ff charmm36-feb2021 -water tip3p -ter -ignh

Using the Charmm36-feb2021 force field in directory charmm36-feb2021.ff

going to rename charmm36-feb2021.ff/merged.r2b
Opening force field file /home/david/Programs/gromacs-2021.1/share/gromacs/top/charmm36-feb2021.ff/merged.r2b
Reading GLU_dipeptide.pdb...
Read '', 14 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 3 residues with 14 atoms

  chain  #res #atoms

  1 'X'     3     14  

All occupancies are one
All occupancies are one
Opening force field file /home/david/Programs/gromacs-2021.1/share/gromacs/top/charmm36-feb2021.ff/atomtypes.atp

Reading residue database... (Charmm36-feb2021)
Opening force field file /home/david/Programs/gromacs-2021.1/share/gromacs/top/charmm36-feb2021.ff/merged.rtp
Opening force field file /home/david/Programs/gromacs-2021.1/share/gromacs/top/charmm36-feb2021.ff/merged.hdb
Opening force field file /home/david/Programs/gromacs-2021.1/share/gromacs/top/charmm36-feb2021.ff/merged.n.tdb
Opening force field file /home/david/Programs/gromacs-2021.1/share/gromacs/top/charmm36-feb2021.ff/merged.c.tdb

Back Off! I just backed up topol.top to ./#topol.top.16#

Processing chain 1 'X' (14 atoms, 3 residues)

Identified residue ACE1 as a starting terminus.

Identified residue NME3 as a ending terminus.
8 out of 8 lines of specbond.dat converted successfully
Select start terminus type for ACE-1
 0: NH3+
 1: NH2
 2: 5TER
 3: None
3
Start terminus ACE-1: None
Select end terminus type for NME-3
 0: COO-
 1: COOH
 2: CT2
 3: 3TER
 4: None
4
End terminus NME-3: None
Opening force field file /home/david/Programs/gromacs-2021.1/share/gromacs/top/charmm36-feb2021.ff/merged.arn

Checking for duplicate atoms....

Generating any missing hydrogen atoms and/or adding termini.

-------------------------------------------------------
Program:     gmx pdb2gmx, version 2021.1
Source file: src/gromacs/gmxpreprocess/pgutil.cpp (line 191)

Fatal error:
Residue 2 named ACE of a molecule in the input file was mapped
to an entry in the topology database, but the atom C used in
that entry is not found in the input file. Perhaps your atom
and/or residue naming needs to be fixed.

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

Please not that the atom numbering in the GLU_dipeptide.pdb file does not play a role or affect the error – the same error occurs when atoms are numbered from 1 in order. The FF used is the same as above (as can be seen).

10

I am getting the exact same problem after using VMD’s psfgen to apply first ACE as I have done previously when running NAMD simulations.

11

I thought i posted the solution i found for the issue; apologies for that.
Its a confusion with the naming.

Solution:
For ACE in the merged.rtp file in charmm36ff directory

image
image889×749 49.2 KB

For NME in the merged.rtp file in charmm36ff directory

image
image843×794 53.2 KB

and i made a simple vim script that i run after capping using pymol

vim -s cap.vim cappedfrompymol.pdb

Contents of cap.vim
image

During pdb2gmx
The -ter flag should be given and none should be selected for both the caps
Works fine for me.

12

Hi,

I’ve spent some time investigating the issue and I think that the problem really lies in the atom names, namely, OY and CY under the [ ACE ] entry. I suspect these cause problems in generating bonds/dihedrals with the following residue, as the atoms are traditionally named O and C, respectively. In older CHARMM force fields (such as charmm27.ff included with GROMACS), these atoms were named O and C, which is why copying the older .rtp entry for [ ACE ] appears to “fix” the issue. However, I think this is wrong, because the atom types for the hydrogen atoms have changed in the meantime.

In addition, there may be another issue in the .hdb file for ACE – the atom names here do not match the .rtp file (i.e., the “old” names are used).

These are just my suspictions, perhaps someone who has deeper knowledge of topology generation could verify these.

David

13

The atom naming is inconsistent. I updated the atom names for ACE to be consistent with CHARMM names to improve interoperability but obviously this broke some core parts of GROMACS in generation of impropers, etc. I am going to have this fixed in the next edition of the CHARMM36 port, as well as rectify the .hdb issue (which was a simple, but consequential, oversight on my part). It may be possible to use the .arn mechanism to internally rename OY->O and CY->C to be compatible with CHARMM-generated inputs and pdb2gmx expectations. I will figure out the best solution in the next port (sometime this month).

14

See my Jul 21. post regarding the temporarily solution to the Ace atom naming problem with CHARMM36

15

I did this, and got
Fatal error:
Residue 2 named ACE of a molecule in the input file was mapped
to an entry in the topology database, but the atom C used in
that entry is not found in the input file. Perhaps your atom
and/or residue naming needs to be fixed.
How to solve this?