[gmx-users] Capping of peptide terminal ends

[Omkar Singh]

Hi all,
I have a peptide system with capinng, N-ACE and C-NAC. i would like to
create a topology file .I tried with pdb2gmx script but it is showing a
fatal error like as;
Fatal error:
atom N not found in buiding block 1ACE while combining tdb and rtp. I
already tried by editing in .rtp entry but after that it is showing error.
I am using CHARMM27 ff/
Select the Force Field:
>From '/usr/local/gromacs/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: CHARMM36 all-atom force field (March 2017)
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 Charmm27 force field in directory charmm27.ff

Opening force field file
/usr/local/gromacs/share/gromacs/top/charmm27.ff/aminoacids.r2b
Opening force field file
/usr/local/gromacs/share/gromacs/top/charmm27.ff/rna.r2b
Reading a3k1.pdb...
Read 'Structure1', 64 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 6 residues with 64 atoms

  chain  #res #atoms
  1 ' '     6     64

All occupancies are one
Opening force field file
/usr/local/gromacs/share/gromacs/top/charmm27.ff/atomtypes.atp
Atomtype 213
Reading residue database... (charmm27)
Opening force field file
/usr/local/gromacs/share/gromacs/top/charmm27.ff/aminoacids.rtp
Residue 44
Sorting it all out...
Opening force field file
/usr/local/gromacs/share/gromacs/top/charmm27.ff/dna.rtp
Residue 48
Sorting it all out...
Opening force field file
/usr/local/gromacs/share/gromacs/top/charmm27.ff/lipids.rtp
Residue 60
Sorting it all out...
Opening force field file
/usr/local/gromacs/share/gromacs/top/charmm27.ff/rna.rtp
Residue 64
Sorting it all out...
Opening force field file
/usr/local/gromacs/share/gromacs/top/charmm27.ff/aminoacids.hdb
Opening force field file
/usr/local/gromacs/share/gromacs/top/charmm27.ff/dna.hdb
Opening force field file
/usr/local/gromacs/share/gromacs/top/charmm27.ff/lipids.hdb
Opening force field file
/usr/local/gromacs/share/gromacs/top/charmm27.ff/rna.hdb
Opening force field file
/usr/local/gromacs/share/gromacs/top/charmm27.ff/aminoacids.n.tdb
Opening force field file
/usr/local/gromacs/share/gromacs/top/charmm27.ff/dna.n.tdb
Opening force field file
/usr/local/gromacs/share/gromacs/top/charmm27.ff/rna.n.tdb
Opening force field file
/usr/local/gromacs/share/gromacs/top/charmm27.ff/aminoacids.c.tdb
Opening force field file
/usr/local/gromacs/share/gromacs/top/charmm27.ff/dna.c.tdb
Opening force field file
/usr/local/gromacs/share/gromacs/top/charmm27.ff/rna.c.tdb

Back Off! I just backed up topol.top to ./#topol.top.8#
Processing chain 1 (64 atoms, 6 residues)
Identified residue ACE1 as a starting terminus.
Identified residue CT35 as a ending terminus.
8 out of 8 lines of specbond.dat converted successfully
Start terminus ACE-1: NH3+
End terminus CT3-5: CT3

-------------------------------------------------------
Program:     gmx pdb2gmx, version 2016.2
Source file: src/gromacs/gmxpreprocess/pdb2top.cpp (line 1127)

Fatal error:
atom N not found in buiding block 1ACE while combining tdb and rtp

I'll be greatfull for any kind of suggestions.