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?
My pdb file looks like this:
HETATM 1 N1 DPHE 1 1.924 -0.229 2.121 1.00 0.00 N
HETATM 2 C1 DPHE 1 1.379 -0.029 0.772 1.00 0.00 C
HETATM 3 H1 DPHE 1 1.257 -0.996 0.283 1.00 0.00 H
HETATM 4 C2 DPHE 1 2.339 0.838 -0.043 1.00 0.00 C
HETATM 5 C3 DPHE 1 3.637 0.098 -0.244 1.00 0.00 C
HETATM 6 C4 DPHE 1 3.804 -0.718 -1.347 1.00 0.00 C
HETATM 7 C5 DPHE 1 4.994 -1.396 -1.531 1.00 0.00 C
HETATM 8 C6 DPHE 1 6.018 -1.258 -0.611 1.00 0.00 C
HETATM 9 C7 DPHE 1 5.851 -0.442 0.491 1.00 0.00 C
HETATM 10 C8 DPHE 1 4.662 0.240 0.673 1.00 0.00 C
HETATM 11 C9 DPHE 1 0.040 0.657 0.868 1.00 0.00 C
HETATM 12 O1 DPHE 1 -0.256 1.270 1.872 1.00 0.00 O
HETATM 13 N2 DPHE 1 -0.827 0.590 -0.162 1.00 0.00 N
HETATM 14 C10 DPHE 1 -2.128 1.258 -0.068 1.00 0.00 C
HETATM 15 H2 DPHE 1 -2.491 1.203 0.958 1.00 0.00 H
HETATM 16 C11 DPHE 1 -3.124 0.565 -1.000 1.00 0.00 C
HETATM 17 C12 DPHE 1 -3.364 -0.844 -0.521 1.00 0.00 C
HETATM 18 C13 DPHE 1 -4.379 -1.104 0.380 1.00 0.00 C
HETATM 19 C14 DPHE 1 -4.598 -2.397 0.819 1.00 0.00 C
HETATM 20 C15 DPHE 1 -3.803 -3.428 0.356 1.00 0.00 C
HETATM 21 C16 DPHE 1 -2.788 -3.168 -0.546 1.00 0.00 C
HETATM 22 C17 DPHE 1 -2.572 -1.876 -0.988 1.00 0.00 C
HETATM 23 C18 DPHE 1 -1.981 2.702 -0.473 1.00 0.00 C
HETATM 24 O2 DPHE 1 -0.902 3.130 -0.806 1.00 0.00 O
HETATM 25 O3 DPHE 1 -3.051 3.513 -0.465 1.00 0.00 O
HETATM 26 H3 DPHE 1 2.019 0.687 2.534 1.00 0.00 H
HETATM 27 H4 DPHE 1 1.216 -0.714 2.652 1.00 0.00 H
HETATM 28 H5 DPHE 1 1.894 1.060 -1.013 1.00 0.00 H
HETATM 29 H6 DPHE 1 2.531 1.769 0.491 1.00 0.00 H
HETATM 30 H7 DPHE 1 3.005 -0.825 -2.065 1.00 0.00 H
HETATM 31 H8 DPHE 1 5.125 -2.034 -2.392 1.00 0.00 H
HETATM 32 H9 DPHE 1 6.947 -1.789 -0.755 1.00 0.00 H
HETATM 33 H10 DPHE 1 6.650 -0.334 1.210 1.00 0.00 H
HETATM 34 H11 DPHE 1 4.532 0.878 1.534 1.00 0.00 H
HETATM 35 H12 DPHE 1 -0.589 0.101 -0.964 1.00 0.00 H
HETATM 36 H13 DPHE 1 -4.066 1.115 -0.998 1.00 0.00 H
HETATM 37 H14 DPHE 1 -2.719 0.541 -2.012 1.00 0.00 H
HETATM 38 H15 DPHE 1 -5.000 -0.298 0.741 1.00 0.00 H
HETATM 39 H16 DPHE 1 -5.391 -2.600 1.524 1.00 0.00 H
HETATM 40 H17 DPHE 1 -3.974 -4.438 0.700 1.00 0.00 H
HETATM 41 H18 DPHE 1 -2.167 -3.974 -0.907 1.00 0.00 H
HETATM 42 H19 DPHE 1 -1.779 -1.673 -1.693 1.00 0.00 H
HETATM 43 H20 DPHE 1 -2.957 4.440 -0.725 1.00 0.00 H
CONECT 1 2 26 27
CONECT 2 1 3 4 11
CONECT 3 2
CONECT 4 2 5 28 29
CONECT 5 4 6 10
CONECT 6 5 7 30
CONECT 7 6 8 31
CONECT 8 7 9 32
CONECT 9 8 10 33
CONECT 10 9 5 34
CONECT 11 2 12 13
CONECT 12 11
CONECT 13 11 14 35
CONECT 14 13 15 16 23
CONECT 15 14
CONECT 16 14 17 36 37
CONECT 17 16 18 22
CONECT 18 17 19 38
CONECT 19 18 20 39
CONECT 20 19 21 40
CONECT 21 20 22 41
CONECT 22 21 17 42
CONECT 23 14 24 25
CONECT 24 23
CONECT 25 23 43
CONECT 26 1
CONECT 27 1
CONECT 28 4
CONECT 29 4
CONECT 30 6
CONECT 31 7
CONECT 32 8
CONECT 33 9
CONECT 34 10
CONECT 35 13
CONECT 36 16
CONECT 37 16
CONECT 38 18
CONECT 39 19
CONECT 40 20
CONECT 41 21
CONECT 42 22
CONECT 43 25
END
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.
Thank you for your reply,
I checked the aminoacids.rtp and there is the DPHE. However, when I run pdb2gmx with my dipeptide I get this error:
Processing chain 1 (40 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.
9 out of 9 lines of specbond.dat converted successfully
Opening force field file /lustre/miifs01/project/m2_komet331hpc/xenidisv/phd/1st_project/2024/gromacs_project/lphe-lphe/charmm36m.ff/aminoacids.arn
Checking for duplicate atoms…
Now there are 38 atoms. Deleted 2 duplicates.
Generating any missing hydrogen atoms and/or adding termini.
Program: gmx pdb2gmx, version 2024.4
Source file: src/gromacs/gmxpreprocess/genhydro.cpp (line 398)
Fatal error:
Atom -C not found in residue DPHE 0, rtp entry DPHE while adding hydrogens
For more information and tips for troubleshooting, please check the GROMACS
website at Common errors when using GROMACS - GROMACS 2024.4 documentation
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.
Hello, thank you for your answer. So I tried another approach to create the pdb file without hydrogen atoms and let pdb2gmx fill them out. This is my new pdb file made in chimera:
SEQRES 1 A 2 DPHE DPHE
HEADER DPHEDIPEPTIDE STRUCTURE
ATOM 1 N DPHEA 1 0.788 -3.513 1.784 1.00 0.00 N
ATOM 2 CA DPHEA 1 0.312 -2.832 0.596 1.00 0.00 C
ATOM 3 C DPHEA 1 0.835 -1.403 0.596 1.00 0.00 C
ATOM 4 O DPHEA 1 1.728 -1.067 1.372 1.00 0.00 O
ATOM 5 CB DPHEA 1 0.864 -3.532 -0.636 1.00 0.00 C
ATOM 6 CG DPHEA 1 0.606 -5.019 -0.689 1.00 0.00 C
ATOM 7 CD1 DPHEA 1 -0.468 -5.517 -1.437 1.00 0.00 C
ATOM 8 CD2 DPHEA 1 1.441 -5.900 0.008 1.00 0.00 C
ATOM 9 CE2 DPHEA 1 1.202 -7.279 -0.041 1.00 0.00 C
ATOM 10 CZ DPHEA 1 0.128 -7.776 -0.789 1.00 0.00 C
ATOM 11 CE1 DPHEA 1 -0.707 -6.896 -1.486 1.00 0.00 C
ATOM 12 N DPHEA 2 0.276 -0.561 -0.277 1.00 0.00 N
ATOM 13 CA DPHEA 2 0.686 0.825 -0.374 1.00 0.00 C
ATOM 14 C DPHEA 2 2.145 0.885 -0.804 1.00 0.00 C
ATOM 15 O DPHEA 2 2.395 0.599 -1.973 1.00 0.00 O
ATOM 16 OXT DPHEA 2 2.965 1.214 0.050 1.00 0.00 O
ATOM 17 CB DPHEA 2 -0.162 1.581 -1.385 1.00 0.00 C
ATOM 18 CG DPHEA 2 0.029 1.154 -2.821 1.00 0.00 C
ATOM 19 CD1 DPHEA 2 -0.869 0.255 -3.409 1.00 0.00 C
ATOM 20 CD2 DPHEA 2 1.104 1.656 -3.563 1.00 0.00 C
ATOM 21 CE2 DPHEA 2 1.281 1.260 -4.894 1.00 0.00 C
ATOM 22 CZ DPHEA 2 0.383 0.361 -5.483 1.00 0.00 C
ATOM 23 CE1 DPHEA 2 -0.692 -0.141 -4.740 1.00 0.00 C
TER 24 DPHEA 2
END
And the error I get relates to OXT atom, which I guess is the Carboxyl group?
Gromacs output:
Back Off! I just backed up topol.top to ./#topol.top.3#
Processing chain 1 ‘A’ (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 2 was not found in rtp entry DPHE with 20 atoms
while sorting atoms.
.
For more information and tips for troubleshooting, please check the GROMACS
website at Common Errors — GROMACS webpage https://www.gromacs.org documentation
Please provide the full pdb2gmx output from the terminal, including your command line.
Sorry, ofcourse. Quick note I have copy-pasted charmm36 into the folder of the default force fields (this means I have 16 instead of the default 15 force fields), thats why I select directly number 8 which is charmm36 (and I don’t have to do export GMXLIB):
(base) vasileios@Laptop-MD:~/Desktop/d-phe$ gmx pdb2gmx -f test.pdb -o processed.gro -p topol.top -water tip3p
:-) 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 test.pdb -o processed.gro -p topol.top -water tip3p
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
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 test.pdb…
Read ‘DPHEDIPEPTIDE STRUCTURE’, 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 ‘A’ 2 23
All occupancies are one
All occupancies are one
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
Processing chain 1 ‘A’ (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 2 was not found in rtp entry DPHE with 20 atoms
while sorting atoms.
.
Also, I wanted to ask, since I will be simulating D-D phenylalanine dipeptide do I have to create in the residuetypes.dat file an entry about DPHE = protein?
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 :)