[gmx-users] Simulation of an acetylated peptide covalently bound to a protein
Zixian Li
zixianli at gmail.com
Sun Jul 2 20:19:20 CEST 2017
Hi Gromacs community,
I get stuck in a simulation of an acetylated peptide covalently bound to a
protein. Could someone please give me some insight?
My system consists of a short peptide bound to a protein. The peptide has 4
amino acids, with the N-terminal Val acetylated and the C-terminal Asp
bound to a Cys residue of a protein. A thioester bond is formed between the
backbone carboxyl group of Asp and the thiol group of Cys.
The scheme below shows the peptide-protein connection
(ACE-Val-Glu-Ile-Asp-CO---S-Cys...).
Protein: N-terminal-...-Ala162-Cys163-Arg164-...-C-terminal
.............................................|..............
...............................
............................................S...............
.............................
.............................................|..............
...............................
Peptide:..ACE-Val-Glu-Ile-N-C-C=O........................................
..........................................|.................
...............................
.........................................CH2................
...........................
..........................................I.................
..............................
......................................O-C=O.................
.........................
To simplify my system for test, I only kept Ala162, Cys163 and Arg164 the
three residues of the protein chain in addition to the bound peptide. I use
Gromacs version 4.6.2 with GROMOS 54A7 force field to do the simulation. I
copied the gromos54a7 folder from the topology library to my local working
directory and renamed it as gromos54a7_thioester. The specbond.dat file was
also copied to the local force field folder.
For the covalent linkage, I acquired the bonded parameters from Automated
Topology Builder (ATB) and Repository server. I submitted an all-atom
Asp-Cys dipeptide linked by thioester bond to ATB for bond length, angle
and dihedral parameters. In the ffbonded.itp file, I added the bond
parameters for the thioester linkage based on the ATB calculations.
;
#define gb_53 0.1780 5.9400e+06
;thioester bond S-C
;
#define ga_55 124.00 3074.03
;O1 C SG
;
#define gd_46 180.000 1.00 3
;CA CB SG C
#define gd_47 180.000 5.86 2
;CA C SG CB
;
#define gd_48 180.000 1.00 6
;N CA C SG
I tried 2 ways to get the topology for the protein with a acetylated
peptide branch. Here are the problems I'm struggling with.
###
Way 1: Specify None for the peptide C-terminal with the hope for
establishing the linkage by specbond.dat file.
pdb2gmx -f Ala162-Cys163-Arg164_res300-ASP304.pdb -o CYS-ASP.gro -water spc
-ff gromos54a7_thioester -merge interactive -ter
Using the Gromos54a7_thioester force field in directory
./gromos54a7_thioester.ff
Opening force field file ./gromos54a7_thioester.ff/aminoacids.r2b
Reading Ala162-Cys163-Arg164_res300-ASP304_1p8A.pdb...
WARNING: all CONECT records are ignored
Read 58 atoms
Analyzing pdb file
Splitting chemical chains based on TER records or chain id changing.
Merge chain ending with residue ARG164 (chain id 'E', atom 22 NH2) and
chain starting with
residue ACE300 (chain id 'E', atom 24 CA) into a single moleculetype
(keeping termini)? [n/y]
y
Merged chains into joint molecule definitions at 1 places.
There are 1 chains and 0 blocks of water and 304 residues with 58 atoms
chain #res #atoms
1 'E' 8 58
All occupancies are one
Opening force field file ./gromos54a7_thioester.ff/atomtypes.atp
Atomtype 1
Reading residue database... (gromos54a7_thioester)
Opening force field file ./gromos54a7_thioester.ff/aminoacids.rtp
Using default: not generating all possible dihedrals
Using default: excluding 3 bonded neighbors
Using default: generating 1,4 H--H interactions
Using default: removing proper dihedrals found on the same bond as a proper
dihedral
Residue 108
Sorting it all out...
Opening force field file ./gromos54a7_thioester.ff/aminoacids.hdb
Opening force field file ./gromos54a7_thioester.ff/aminoacids.n.tdb
Opening force field file ./gromos54a7_thioester.ff/aminoacids.c.tdb
Processing chain 1 'E' (58 atoms, 8 residues)
Identified residue ALA162 as a starting terminus.
Identified residue ARG164 as a ending terminus.
Identified residue ACE300 as a starting terminus.
Identified residue ASP304 as a ending terminus.
8 out of 8 lines of specbond.dat converted successfully
Select start terminus type for ALA-162
0: NH3+
1: NH2
2: None
0
Start terminus ALA-162: NH3+
Select end terminus type for ARG-164
0: COO-
1: COOH
2: None
0
End terminus ARG-164: COO-
Select start terminus type for ACE-300
0: NH3+
1: NH2
2: None
2
Start terminus ACE-300: None
Select end terminus type for ASP-304
0: COO-
1: COOH
2: None
2
End terminus ASP-304: None
-------------------------------------------------------
Program pdb2gmx, VERSION 4.6.2
Source code file:
/home/zixian/Downloads/gromacs-4.6.2/src/kernel/pdb2top.c, line: 1109
Fatal error:
There is a dangling bond at at least one of the terminal ends. Fix your
coordinate file, add a new terminal database entry (.tdb), or select the
proper existing terminal entry.
If the SG-C bond is recognized by Gromacs, it should not say a dangling
bond at terminal ends. However, the SG-C bond added in specbond.dat file
was ignored by the program. I checked the input pdb file in pymol about the
S-C distance. It's actually 0.18 nm.
Below is my specbond.dat file. The last line was added by me.
9
CYS SG 1 CYS SG 1 0.2 CYS2 CYS2
CYS SG 1 HEM FE 2 0.25 CYS2 HEME
CYS SG 1 HEM CAB 1 0.18 CYS2 HEME
CYS SG 1 HEM CAC 1 0.18 CYS2 HEME
HIS NE2 1 HEM FE 1 0.2 HIS1 HEME
MET SD 1 HEM FE 1 0.24 MET HEME
CO C 1 HEME FE 1 0.19 CO HEME
CYM SG 1 CYM SG 1 0.2 CYS2 CYS2
CYS SG 1 ASP C 1 0.18 CYS ASP ;added by user
###
Way 2: I added a [ thioester ] entry in the aminoacid.c.tdb in addition to
the SG-C bond definition to specbond.dat file.
[ thioester ]
[ replace ]
C C C 12.011 0.27
O O1 O 15.9994 -0.45
[ bonds ]
C O1 gb_5
C SG gb_53 ;added by user
[ angles ]
; ai aj ak gromos type
CB SG C ga_4 ; CG SD CE ga_4
CA C SG ga_16 ; CA CB SG ga_16
O1 C SG ga_55 ;
CA C O1 ga_30
[ dihedrals ]
; ai aj ak al gromos type
CA CB SG C gd_46
CA C SG CB gd_47
N CA C SG gd_48
[ impropers ]
C SG CA O gi_1 ; for thioester
pdb2gmx -f Ala162-Cys163-Arg164_res300-ASP304.pdb -o CYS-ASP.gro -p
CYS-ASP.top -i CYS-ASP.itp -water spc -ff gromos54a7_thioester -merge
interactive -ter
Using the Gromos54a7_thioester force field in directory
./gromos54a7_thioester.ff
Opening force field file ./gromos54a7_thioester.ff/aminoacids.r2b
Reading Ala162-Cys163-Arg164_res300-ASP304.pdb...
WARNING: all CONECT records are ignored
Read 58 atoms
Analyzing pdb file
Splitting chemical chains based on TER records or chain id changing.
Merge chain ending with residue ARG164 (chain id 'E', atom 22 NH2) and
chain starting with
residue ACE300 (chain id 'E', atom 24 CA) into a single moleculetype
(keeping termini)? [n/y]
y
Merged chains into joint molecule definitions at 1 places.
There are 1 chains and 0 blocks of water and 304 residues with 58 atoms
chain #res #atoms
1 'E' 8 58
All occupancies are one
Opening force field file ./gromos54a7_thioester.ff/atomtypes.atp
Atomtype 1
Reading residue database... (gromos54a7_thioester)
Opening force field file ./gromos54a7_thioester.ff/aminoacids.rtp
Using default: not generating all possible dihedrals
Using default: excluding 3 bonded neighbors
Using default: generating 1,4 H--H interactions
Using default: removing proper dihedrals found on the same bond as a proper
dihedral
Residue 108
Sorting it all out...
Opening force field file ./gromos54a7_thioester.ff/aminoacids.hdb
Opening force field file ./gromos54a7_thioester.ff/aminoacids.n.tdb
Opening force field file ./gromos54a7_thioester.ff/aminoacids.c.tdb
Processing chain 1 'E' (58 atoms, 8 residues)
Identified residue ALA162 as a starting terminus.
Identified residue ARG164 as a ending terminus.
Identified residue ACE300 as a starting terminus.
Identified residue ASP304 as a ending terminus.
8 out of 8 lines of specbond.dat converted successfully
Select start terminus type for ALA-162
0: NH3+
1: NH2
2: None
0
Start terminus ALA-162: NH3+
Select end terminus type for ARG-164
0: COO-
1: COOH
2: thioester
3: None
0
End terminus ARG-164: COO-
Select start terminus type for ACE-300
0: NH3+
1: NH2
2: None
2
Start terminus ACE-300: None
Select end terminus type for ASP-304
0: COO-
1: COOH
2: thioester
3: None
2
End terminus ASP-304: thioester
Checking for duplicate atoms....
Generating any missing hydrogen atoms and/or adding termini.
Now there are 8 residues with 73 atoms
Making bonds...
Number of bonds was 76, now 71
Generating angles, dihedrals and pairs...
Before cleaning: 120 pairs
-------------------------------------------------------
Program pdb2gmx, VERSION 4.6.2
Source code file: /home/zixian/Downloads/gromacs-4.6.2/src/kernel/pgutil.c,
line: 126
Fatal error:
Residue 8 named ASP of a molecule in the input file was mapped
to an entry in the topology database, but the atom SG used in
an interaction of type improper in that entry is not found in the
input file. Perhaps your atom and/or residue naming needs to be
fixed.
The SG-C bond defined in specbond.dat was skipped again for unknown
reasons. This time the program seems treat SG as part of ASP because of the
SG-C bond, however, SG belongs to Cys.
I really appreciate your diagnosis.
Thanks,
Zixian Li
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