[gmx-users] Fatal error: Atom O4 in residue GLU 7 was not found in rtp entry

Fri Sep 6 10:36:27 CEST 2019

Hello Everyone!

I am trying to simulate five peptides along with water using GROMACS.
I have used the PACKMOL to prepare initail PDB files.
Peptide were made using Schrodinger Maestro.
I have got a final PDB file having the water molecules and randowmly
distributed peptides.

After that I am using command pdb2gmx using the CHARMM36 force field.

Following are the commands and its output,

-------------------------------------------------------------------------------------------------------------
gmx pdb2gmx -f final.pdb -o final.gro -water spce -ignh -ter
                     :-) GROMACS - gmx pdb2gmx, 2018.4 (-:

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GROMACS:      gmx pdb2gmx, version 2018.4
Executable:   /usr/local/gromacs/bin/gmx
Data prefix:  /usr/local/gromacs
Working dir:  /home/navneet/Desktop/amyloid
Command line:
  gmx pdb2gmx -f final.pdb -o final.gro -water spce -ignh -ter

Select the Force Field:
>From current directory:
 1: CHARMM36 all-atom force field (March 2019)
>From '/usr/local/gromacs/share/gromacs/top':
 2: AMBER03 protein, nucleic AMBER94 (Duan et al., J. Comp. Chem. 24,
1999-2012, 2003)
 3: AMBER94 force field (Cornell et al., JACS 117, 5179-5197, 1995)
 4: AMBER96 protein, nucleic AMBER94 (Kollman et al., Acc. Chem. Res. 29,
461-469, 1996)
 5: AMBER99 protein, nucleic AMBER94 (Wang et al., J. Comp. Chem. 21,
1049-1074, 2000)
 6: AMBER99SB protein, nucleic AMBER94 (Hornak et al., Proteins 65,
712-725, 2006)
 7: AMBER99SB-ILDN protein, nucleic AMBER94 (Lindorff-Larsen et al.,
Proteins 78, 1950-58, 2010)
 8: AMBERGS force field (Garcia & Sanbonmatsu, PNAS 99, 2782-2787, 2002)
 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: GROMOS96 54a7 force field (Eur. Biophys. J. (2011), 40,, 843-856, DOI:
10.1007/s00249-011-0700-9)
17: GROMOS96 54a7 force field (Eur. Biophys. J. (2011), 40,, 843-856, DOI:
10.1007/s00249-011-0700-9)
18: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)
1

Using the Charmm36-mar2019 force field in directory ./charmm36-mar2019.ff

Opening force field file ./charmm36-mar2019.ff/merged.r2b
Reading final.pdb...
Read 'Built with Packmol through Packmol Memgen', 5305 atoms
Analyzing pdb file
Splitting chemical chains based on TER records or chain id changing.
There are 1 chains and 1 blocks of water and 5035 residues with 5305 atoms

  chain  #res #atoms
  1 'A'    35    305
  2 ' '  5000   5000  (only water)

WARNING: there were 5000 atoms with zero occupancy and 0 atoms with
         occupancy unequal to one (out of 5305 atoms). Check your pdb file.

Opening force field file ./charmm36-mar2019.ff/atomtypes.atp
Atomtype 447
Reading residue database... (charmm36-mar2019)
Opening force field file ./charmm36-mar2019.ff/merged.rtp
Residue 1318
Sorting it all out...
Opening force field file ./charmm36-mar2019.ff/merged.hdb
Opening force field file ./charmm36-mar2019.ff/merged.n.tdb
Opening force field file ./charmm36-mar2019.ff/merged.c.tdb

Back Off! I just backed up topol.top to ./#topol.top.2#
Processing chain 1 'A' (305 atoms, 35 residues)
Identified residue LYS1 as a starting terminus.
Identified residue GLU7 as a ending terminus.
8 out of 8 lines of specbond.dat converted successfully
Select start terminus type for LYS-1
 0: NH3+
 1: NH2
 2: 5TER
 3: None
1
Start terminus LYS-1: NH2
Select end terminus type for GLU-7
 0: COO-
 1: COOH
 2: CT2
 3: 3TER
 4: None
1
End terminus GLU-7: COOH
Opening force field file ./charmm36-mar2019.ff/merged.arn

-------------------------------------------------------
Program:     gmx pdb2gmx, version 2018.4
Source file: src/gromacs/gmxpreprocess/pdb2gmx.cpp (line 753)

Fatal error:
Atom O4 in residue GLU 7 was not found in rtp entry GLU with 15 atoms
while sorting atoms.
.

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

Please help in solving this error.

     Thanks & Regards
_______________________________________________________

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*NAVNEET KUMAR*

Doctoral Student
Dept. of Pharmacoinformatics
National Institute of Pharmaceutical Education and Research, Sector 67,
S.A.S. Nagar - 160062, Punjab (INDIA)
P +918017967647  <+918017967647> |
E navneetcdl at gmail.com  <navneetcdl at gmail.com>

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