[gmx-users] Capping of peptide terminal ends

Justin Lemkul jalemkul at vt.edu
Fri Oct 12 17:06:01 CEST 2018



On 10/12/18 6:35 AM, Omkar Singh wrote:
> 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

You need to specify "None" for both termini, otherwise pdb2gmx tries to 
patch them as normal amino acids. The ACE and CT3 need to be present in 
the input coordinate file as separate residues, appropriately named.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com

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