GROMACS version: 2024.4
GROMACS modification: No
Hello! I’m new to molecular simulations and need some guidance. I want to simulate dipeptides composed of D-amino acids using the CHARMM36 force field in GROMACS. I’ve created the PDB file of my dipeptide using PyMOL. What are the steps I should follow to ensure GROMACS can read and simulate the system correctly?
Hi @b-omics
I am not super familiar with parametrization of proteins, but for sure if you want to use CHARMM36m then a very good starting point is the CHARMM-GUI website where you can load your pdb and have the webserver parametrize it for you.
I never did it for special aminoacids so I do not know if you can find what you need, but there are also a few tutorials on the website itself that will help you. You can also do it with gmx pdb2gmx if you have the CHARMM36m new forcefield distro. That might be more complex if you are new to GROMACS way of formatting files, but there are also old posts that can address problems that you may face in this case.
CHARMM36 already supports D-amino acids. You do not have to do anything special. The amino acid names are DXXX, where XXX is the conventional amino acid name. So your DPHE should run through pdb2gmx with no problem, like any other residue.
The error means the naming of the residue that precedes DPHE does not conform to typical amino acid nomenclature (C is the amide carbon atom). If DPHE is the first residue in the chain, you need to specify an appropriate terminus patch. Providing the full terminal output from pdb2gmx and a better description of what is in your input file would be helpful for troubleshooting.
Please provide the full pdb2gmx output from the terminal, including your command line.
Use the -ter option and make sure to select the NTER and CTER patches for the termini; the problem is likely coming from incorrect interpretation of the C-terminus.
Given that you only have two DPHE in the system, it is irrelevant whether you specify them as protein or not.
Hi, when I run this command, I don’t get prompted to select NTER and CTER, what am I doing wrong? Also, If I add DPHE=protein in residuetypes.dat file it works without -ter command. What would you recommend to do to fix this problem?:
gmx pdb2gmx -f d-d-phe.pdb -o processed.gro -p topol.top -ter
:-) GROMACS - gmx pdb2gmx, 2023.3-Ubuntu_2023.3_1ubuntu3 (-:
Executable: /usr/bin/gmx
Data prefix: /usr
Working dir: /home/vasileios/Desktop/d-phe
Command line:
gmx pdb2gmx -f d-d-phe.pdb -o processed.gro -p topol.top -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: CHARMM all-atom force field
9: CHARMM27 all-atom force field (CHARM22 plus CMAP for proteins)
10: GROMOS96 43a1 force field
11: GROMOS96 43a2 force field (improved alkane dihedrals)
12: GROMOS96 45a3 force field (Schuler JCC 2001 22 1205)
13: GROMOS96 53a5 force field (JCC 2004 vol 25 pag 1656)
14: GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656)
15: GROMOS96 54a7 force field (Eur. Biophys. J. (2011), 40, 843-856, DOI: 10.1007/s00249-011-0700-9)
16: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)
8
Using the Charmm36-jul2022 force field in directory charmm36-jul2022.ff
Opening force field file /usr/share/gromacs/top/charmm36-jul2022.ff/watermodels.dat
Select the Water Model:
1: TIP3P CHARMM-modified TIP3P water model (recommended over original TIP3P)
2: TIP3P_ORIGINAL Original TIP3P water model
3: SPC SPC water model
4: SPCE SPC/E water model
5: TIP5P TIP5P water model
6: TIP4P TIP4P water model
7: TIP4PEW TIP4P/Ew water model
8: None
1
going to rename charmm36-jul2022.ff/aminoacids.r2b
Opening force field file /usr/share/gromacs/top/charmm36-jul2022.ff/aminoacids.r2b
going to rename charmm36-jul2022.ff/carb.r2b
Opening force field file /usr/share/gromacs/top/charmm36-jul2022.ff/carb.r2b
going to rename charmm36-jul2022.ff/cgenff.r2b
Opening force field file /usr/share/gromacs/top/charmm36-jul2022.ff/cgenff.r2b
going to rename charmm36-jul2022.ff/ethers.r2b
Opening force field file /usr/share/gromacs/top/charmm36-jul2022.ff/ethers.r2b
going to rename charmm36-jul2022.ff/lipid.r2b
Opening force field file /usr/share/gromacs/top/charmm36-jul2022.ff/lipid.r2b
going to rename charmm36-jul2022.ff/metals.r2b
Opening force field file /usr/share/gromacs/top/charmm36-jul2022.ff/metals.r2b
going to rename charmm36-jul2022.ff/na.r2b
Opening force field file /usr/share/gromacs/top/charmm36-jul2022.ff/na.r2b
going to rename charmm36-jul2022.ff/silicates.r2b
Opening force field file /usr/share/gromacs/top/charmm36-jul2022.ff/silicates.r2b
going to rename charmm36-jul2022.ff/solvent.r2b
Opening force field file /usr/share/gromacs/top/charmm36-jul2022.ff/solvent.r2b
Reading d-d-phe.pdb…
Read ‘’, 23 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 2 residues with 23 atoms
chain #res #atoms
1 ’ ’ 2 23
there were 2 atoms with zero occupancy and 19 atoms with occupancy unequal to one (out of 23 atoms). Check your pdb file.
there were 2 atoms with zero occupancy and 19 atoms with occupancy unequal to one (out of 23 atoms). Check your pdb file.
Opening force field file /usr/share/gromacs/top/charmm36-jul2022.ff/atomtypes.atp
Reading residue database… (Charmm36-jul2022)
Opening force field file /usr/share/gromacs/top/charmm36-jul2022.ff/aminoacids.rtp
Opening force field file /usr/share/gromacs/top/charmm36-jul2022.ff/carb.rtp
Opening force field file /usr/share/gromacs/top/charmm36-jul2022.ff/cgenff.rtp
Opening force field file /usr/share/gromacs/top/charmm36-jul2022.ff/ethers.rtp
Opening force field file /usr/share/gromacs/top/charmm36-jul2022.ff/lipid.rtp
Opening force field file /usr/share/gromacs/top/charmm36-jul2022.ff/metals.rtp
Opening force field file /usr/share/gromacs/top/charmm36-jul2022.ff/na.rtp
Opening force field file /usr/share/gromacs/top/charmm36-jul2022.ff/silicates.rtp
Opening force field file /usr/share/gromacs/top/charmm36-jul2022.ff/solvent.rtp
Opening force field file /usr/share/gromacs/top/charmm36-jul2022.ff/aminoacids.hdb
Opening force field file /usr/share/gromacs/top/charmm36-jul2022.ff/carb.hdb
Opening force field file /usr/share/gromacs/top/charmm36-jul2022.ff/cgenff.hdb
Opening force field file /usr/share/gromacs/top/charmm36-jul2022.ff/ethers.hdb
Opening force field file /usr/share/gromacs/top/charmm36-jul2022.ff/lipid.hdb
Opening force field file /usr/share/gromacs/top/charmm36-jul2022.ff/metals.hdb
Opening force field file /usr/share/gromacs/top/charmm36-jul2022.ff/na.hdb
Opening force field file /usr/share/gromacs/top/charmm36-jul2022.ff/silicates.hdb
Opening force field file /usr/share/gromacs/top/charmm36-jul2022.ff/solvent.hdb
Opening force field file /usr/share/gromacs/top/charmm36-jul2022.ff/aminoacids.n.tdb
Opening force field file /usr/share/gromacs/top/charmm36-jul2022.ff/carb.n.tdb
Opening force field file /usr/share/gromacs/top/charmm36-jul2022.ff/cgenff.n.tdb
Opening force field file /usr/share/gromacs/top/charmm36-jul2022.ff/ethers.n.tdb
Opening force field file /usr/share/gromacs/top/charmm36-jul2022.ff/lipid.n.tdb
Opening force field file /usr/share/gromacs/top/charmm36-jul2022.ff/metals.n.tdb
Opening force field file /usr/share/gromacs/top/charmm36-jul2022.ff/na.n.tdb
Opening force field file /usr/share/gromacs/top/charmm36-jul2022.ff/silicates.n.tdb
Opening force field file /usr/share/gromacs/top/charmm36-jul2022.ff/solvent.n.tdb
Opening force field file /usr/share/gromacs/top/charmm36-jul2022.ff/aminoacids.c.tdb
Opening force field file /usr/share/gromacs/top/charmm36-jul2022.ff/carb.c.tdb
Opening force field file /usr/share/gromacs/top/charmm36-jul2022.ff/cgenff.c.tdb
Opening force field file /usr/share/gromacs/top/charmm36-jul2022.ff/ethers.c.tdb
Opening force field file /usr/share/gromacs/top/charmm36-jul2022.ff/lipid.c.tdb
Opening force field file /usr/share/gromacs/top/charmm36-jul2022.ff/metals.c.tdb
Opening force field file /usr/share/gromacs/top/charmm36-jul2022.ff/na.c.tdb
Opening force field file /usr/share/gromacs/top/charmm36-jul2022.ff/silicates.c.tdb
Opening force field file /usr/share/gromacs/top/charmm36-jul2022.ff/solvent.c.tdb
Back Off! I just backed up topol.top to ./#topol.top.2#
Processing chain 1 (23 atoms, 2 residues)
Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior.
8 out of 8 lines of specbond.dat converted successfully
Opening force field file /usr/share/gromacs/top/charmm36-jul2022.ff/aminoacids.arn
Program: gmx pdb2gmx, version 2023.3-Ubuntu_2023.3_1ubuntu3
Source file: src/gromacs/gmxpreprocess/pdb2gmx.cpp (line 870)
Fatal error:
Atom OXT in residue DPHE 0 was not found in rtp entry DPHE with 20 atoms
while sorting atoms.
I would do this :)
Did you unzip the CHARMM36 force field in your working folder, because it supposed to be listed as number 1 in your list of forcefields.
gmx pdb2gmx -v -f peptide.pdb -o peptide.gro -p topol.top -water tip3p -ter -ignh
thank you for your reply. Yes