[gmx-users] Capping of peptide terminal ends
Omkar Singh
omkantnirala92 at gmail.com
Sun Oct 14 06:48:45 CEST 2018
Hi ,
I did same as you suggest me, but now new error is coming as shown below.
I just backed up topol.top to ./#topol.top.30#
Processing chain 1 (64 atoms, 7 residues)
Identified residue ACE0 as a starting terminus.
Identified residue CT31 as a ending terminus.
8 out of 8 lines of specbond.dat converted successfully
Select start terminus type for ACE-0
0: NH3+
1: NH2
2: None
2
Start terminus ACE-0: None
Select end terminus type for CT3-1
0: CT3
1: COO-
2: COOH
3: CT2
4: None
4
End terminus CT3-1: None
Opening force field file
/usr/local/gromacs/share/gromacs/top/charmm27.ff/aminoacids.arn
Opening force field file
/usr/local/gromacs/share/gromacs/top/charmm27.ff/dna.arn
Opening force field file
/usr/local/gromacs/share/gromacs/top/charmm27.ff/rna.arn
-------------------------------------------------------
Program: gmx pdb2gmx, version 2016.2
Source file: src/gromacs/gmxpreprocess/pdb2gmx.cpp (line 753)
Fatal error:
Atom H31 in residue ACE 0 was not found in rtp entry ACE with 6 atoms
while sorting atoms.
For a hydrogen, this can be a different protonation state, or it
might have had a different number in the PDB file and was rebuilt
(it might for instance have been H3, and we only expected H1 & H2).
Note that hydrogens might have been added to the entry for the N-terminus.
Remove this hydrogen or choose a different protonation state to solve it.
Option -ignh will ignore all hydrogens in the input.
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
terminal entries are as following
N-terminal
ATOM 3 CH3 ACE 0 8.735 -0.604 2.523 1.00 0.00
C
ATOM 31 H31 ACE 0 9.608 0.044 2.605 1.00 0.00
H
ATOM 32 H32 ACE 0 8.348 -0.783 3.526 1.00 0.00
H
ATOM 33 H33 ACE 0 9.056 -1.553 2.095 1.00 0.00
H
ATOM 2 C ACE 1 7.677 0.041 1.642 1.00 0.00
C
ATOM 4 O ACE 1 7.890 1.122 1.099 1.00 0.00
O
................................................................................................................
C- terminal
ATOM 23 N CT3 1 -5.561 0.819 -3.047 1.00 0.00
N
ATOM 50 HN CT3 1 -5.240 1.762 -2.900 1.00 0.00
H
ATOM 24 CH3 CT3 1 -6.804 0.635 -3.787 1.00 0.00
C
ATOM 51 H31 CT3 1 -7.250 1.599 -4.034 1.00 0.00
H
ATOM 52 H32 CT3 1 -6.624 0.095 -4.718 1.00 0.00
H
ATOM 53 H33 CT3 1 -7.527 0.065 -3.201 1.00 0.00
H
The spacing is fine in real pdb.
On Fri, Oct 12, 2018 at 8:36 PM Justin Lemkul <jalemkul at vt.edu> wrote:
>
>
> 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
>
> --
> ==================================================
>
> 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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