Palmitoylation

User discussions
1

GROMACS version: 2020.1-Ubuntu-2020.1-1

How to N-terminally palmitoylate without errors?

gmx pdb2gmx -f PAMYKK.pdb -o micoa.gro -p micoa.top -water spc -ignh -ter

Select the Force Field:
From ‘/usr/share/gromacs/top’:
1: AMBER03 protein, nucleic AMBER94 (Duan et al., J. Comp. Chem. 24, 1999-2012, 2003)
2: AMBER94 force field (Cornell et al., JACS 117, 5179-5197, 1995)
3: AMBER96 protein, nucleic AMBER94 (Kollman et al., Acc. Chem. Res. 29, 461-469, 1996)
4: AMBER99 protein, nucleic AMBER94 (Wang et al., J. Comp. Chem. 21, 1049-1074, 2000)
5: AMBER99SB protein, nucleic AMBER94 (Hornak et al., Proteins 65, 712-725, 2006)
6: AMBER99SB-ILDN protein, nucleic AMBER94 (Lindorff-Larsen et al., Proteins 78, 1950-58, 2010)
7: AMBERGS force field (Garcia & Sanbonmatsu, PNAS 99, 2782-2787, 2002)
8: CHARMM27 all-atom force field (CHARM22 plus CMAP for proteins)
9: GROMOS96 43a1 force field
10: GROMOS96 43a2 force field (improved alkane dihedrals)
11: GROMOS96 45a3 force field (Schuler JCC 2001 22 1205)
12: GROMOS96 53a5 force field (JCC 2004 vol 25 pag 1656)
13: GROMOS96 54a7 force field (Eur. Biophys. J. (2011), 40, 843-856, DOI: 10.1007/s00249-011-0700-9)
14: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)
8

Using the Charmm27 force field in directory charmm27.ff

Warning: file does not end with a newline, last line:
PAM Protein
going to rename charmm27.ff/aminoacids.r2b
Opening force field file /usr/share/gromacs/top/charmm27.ff/aminoacids.r2b
going to rename charmm27.ff/rna.r2b
Opening force field file /usr/share/gromacs/top/charmm27.ff/rna.r2b
Warning: file does not end with a newline, last line:
PAM Protein
Reading PAMYKK.pdb…
WARNING: all CONECT records are ignored
Read ‘’, 48 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 48 atoms

chain #res #atoms
1 ‘A’ 4 48

All occupancies are one
Opening force field file /usr/share/gromacs/top/charmm27.ff/atomtypes.atp
Reading residue database… (Charmm27)
Opening force field file /usr/share/gromacs/top/charmm27.ff/aminoacids.rtp
Opening force field file /usr/share/gromacs/top/charmm27.ff/dna.rtp
Opening force field file /usr/share/gromacs/top/charmm27.ff/lipids.rtp
Opening force field file /usr/share/gromacs/top/charmm27.ff/rna.rtp
Opening force field file /usr/share/gromacs/top/charmm27.ff/aminoacids.hdb
Opening force field file /usr/share/gromacs/top/charmm27.ff/dna.hdb
Opening force field file /usr/share/gromacs/top/charmm27.ff/lipids.hdb
Opening force field file /usr/share/gromacs/top/charmm27.ff/rna.hdb
Opening force field file /usr/share/gromacs/top/charmm27.ff/aminoacids.n.tdb
Opening force field file /usr/share/gromacs/top/charmm27.ff/dna.n.tdb
Opening force field file /usr/share/gromacs/top/charmm27.ff/rna.n.tdb
Opening force field file /usr/share/gromacs/top/charmm27.ff/aminoacids.c.tdb
Opening force field file /usr/share/gromacs/top/charmm27.ff/dna.c.tdb
Opening force field file /usr/share/gromacs/top/charmm27.ff/rna.c.tdb

Back Off! I just backed up micoa.top to ./#micoa.top.9#
Using the Charmm27 force field in directory charmm27.ff

Warning: file does not end with a newline, last line:
PAM Protein
going to rename charmm27.ff/aminoacids.r2b
Opening force field file /usr/share/gromacs/top/charmm27.ff/aminoacids.r2b
going to rename charmm27.ff/rna.r2b
Opening force field file /usr/share/gromacs/top/charmm27.ff/rna.r2b
Warning: file does not end with a newline, last line:
PAM Protein
Reading PAMYKK.pdb…
WARNING: all CONECT records are ignored
Read ‘’, 48 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 48 atoms

chain #res #atoms
1 ‘A’ 4 48

All occupancies are one
Opening force field file /usr/share/gromacs/top/charmm27.ff/atomtypes.atp
Reading residue database… (Charmm27)
Opening force field file /usr/share/gromacs/top/charmm27.ff/aminoacids.rtp
Opening force field file /usr/share/gromacs/top/charmm27.ff/dna.rtp
Opening force field file /usr/share/gromacs/top/charmm27.ff/lipids.rtp
Opening force field file /usr/share/gromacs/top/charmm27.ff/rna.rtp
Opening force field file /usr/share/gromacs/top/charmm27.ff/aminoacids.hdb
Opening force field file /usr/share/gromacs/top/charmm27.ff/dna.hdb
Opening force field file /usr/share/gromacs/top/charmm27.ff/lipids.hdb
Opening force field file /usr/share/gromacs/top/charmm27.ff/rna.hdb
Opening force field file /usr/share/gromacs/top/charmm27.ff/aminoacids.n.tdb
Opening force field file /usr/share/gromacs/top/charmm27.ff/dna.n.tdb
Opening force field file /usr/share/gromacs/top/charmm27.ff/rna.n.tdb
Opening force field file /usr/share/gromacs/top/charmm27.ff/aminoacids.c.tdb
Opening force field file /usr/share/gromacs/top/charmm27.ff/dna.c.tdb
Opening force field file /usr/share/gromacs/top/charmm27.ff/rna.c.tdb

Back Off! I just backed up micoa.top to ./#micoa.top.9#
Processing chain 1 ‘A’ (48 atoms, 4 residues)
Identified residue PAM0 as a starting terminus.
Identified residue LYS3 as a ending terminus.
8 out of 8 lines of specbond.dat converted successfully
Select start terminus type for PAM-0
0: 5’
1: None
1
Start terminus PAM-0: None
Select end terminus type for LYS-3
0: COO-
1: 3’
2: None
0
End terminus LYS-3: COO-
Opening force field file /usr/share/gromacs/top/charmm27.ff/aminoacids.arn
Opening force field file /usr/share/gromacs/top/charmm27.ff/dna.arn
Opening force field file /usr/share/gromacs/top/charmm27.ff/rna.arn
Checking for duplicate atoms…
Generating any missing hydrogen atoms and/or adding termini.

Program: gmx pdb2gmx, version 2020.1-Ubuntu-2020.1-1
Source file: src/gromacs/gmxpreprocess/pgutil.cpp (line 151)

Fatal error:
Residue 2 named PAM 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.

2

Hi,

Is the PAM residue in your .rtp just a palmitoyl moiety, or a palmitoylated amino acid? The second seems like an easier option to me.

From your output it’s hard to tell, but it might be that the issue is the outgoing bond connecting with the next amino acid (will be defined e.g. with a “C +N” entry in your [ bonds ]). Also make sure that your PAM residue is classified as Protein in residuetypes.dat.

If the error persists, it might help if you provided the initial .pdb and .rtp entry to make sure there are no issues with naming.

Best,
Miłosz

3

Hi Milosz

Thanks for your answer, I tried to add +N but with same error:

Select start terminus type for PAM-0
0: 5’
1: None
1
Start terminus PAM-0: None
Select end terminus type for LYS-3
0: COO-
1: 3’
2: None
0
End terminus LYS-3: COO-
Opening force field file /usr/share/gromacs/top/charmm27.ff/aminoacids.arn
Opening force field file /usr/share/gromacs/top/charmm27.ff/dna.arn
Opening force field file /usr/share/gromacs/top/charmm27.ff/rna.arn
Checking for duplicate atoms…
Generating any missing hydrogen atoms and/or adding termini.

(Attachment aminoacids.n.tdb is missing)

(Attachment aminoacids.rtp is missing)

(Attachment aminoacids.c.tdb is missing)

(Attachment PAMYKK.pdb is missing)

(Attachment micelles.pdb is missing)

4

Hi Milosz

Thanks for your answer, I tried to add +N but with same error:

Select start terminus type for PAM-0
0: 5’
1: None
1
Start terminus PAM-0: None
Select end terminus type for LYS-3
0: COO-
1: 3’
2: None
0
End terminus LYS-3: COO-
Opening force field file /usr/share/gromacs/top/charmm27.ff/aminoacids.arn
Opening force field file /usr/share/gromacs/top/charmm27.ff/dna.arn
Opening force field file /usr/share/gromacs/top/charmm27.ff/rna.arn
Checking for duplicate atoms…
Generating any missing hydrogen atoms and/or adding termini.

5

How about the other questions, is your residuetypes.dat updated? What does your .rtp entry look like, and do the names match these in .pdb? Does your PAM residue include the amino acid itself? This error is pretty generic and can have several causes.

6

Hi Milosz, In fact I resolved this by editing terminal CO residue names. However, now there’s another weird problem. I am trying to simulate micelles. When I run pdb2gmx on a test file of 3 molecules I get a correct .gro file, when I run the exact same command on the actual file of 108 molecules (with the same format, generated in the same way as the file of 3 molecules, only difference is number of ‘chains’ in the micelle) the .gro file has errors, it has introduced COO at the end of the lipid chain (with errors in the O group coordinates) and seems to think it’s a terminus. No idea what is happening, everything is the same except the number of molecules.

7

Could it be the identification of chains? pdb2gmx might recognize chains by either the letter code in the .pdb file (that might run from A to Z) or TER lines at the end of the chain. But it’s also hard to guess without seeing the files and possible issues with naming/formatting/setup. I thought that PAM was your N-terminal residue, so it’s already surprising the issue was with the processing of the C-term in PAM.