[gmx-users] Capping of peptide terminal ends

Discussion:

Omkar Singh

2018-10-12 10:35:11 UTC

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.

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Justin Lemkul

2018-10-12 15:05:47 UTC

Permalink

Post by 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;
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/
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)
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

Omkar Singh

2018-10-14 04:48:30 UTC

Permalink

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.

Post by Omkar Singh

error.

Post by Omkar Singh
I am using CHARMM27 ff/
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,

Post by Omkar Singh
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,
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
http://www.thelemkullab.com
==================================================
--
Gromacs Users mailing list
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
posting!
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or

Justin Lemkul

2018-10-14 12:12:10 UTC

Permalink

Post by Omkar Singh
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)
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

If you follow this link, you will find the exact solution to your problem.

-Justin

Post by Omkar Singh
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.

Post by Omkar Singh

error.

29,

--
==================================================

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

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

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

==================================================

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