Hello, dear Amber authors/users!
I have PDB file which has two proteins. C-terminal end carbon of one
protein is connected via a thioester bond to a sulphur in cysteine of the
other protein.
The force field parameters for thioester bond was obtained from the paper
- "Determination of AMBER Force Field Parameters for Thioester
by Quantum Chemical Calculations, Akifumi Oda, Chem. Lett. 2013, 42,
12061208 "
I created a local copy of the forcefield file and added all these
parameters into the file.
To model this complete system, I tried two methods:-
1) Create a thioester bond between these two residues in UCSF chimera,
imported the PDB file and the modified force field file in leap and
created parameter and topology files.
2) Import the PDB file without thioester bond in the leap, use the BOND
command to create a bond between sulphur and c-terminal carbon. And then
saved the topology and parameter files, without any errors being reported.
Using desc command I also insured that the bonds are created (for both the
scenarios mentioned above).
Now using the ambpdb command I converted the parameter file and topology
file.
The PDB thus created does not have this thioester bond and instead, the
C-terminal was attached to the n-terminal of the other protein with an
unusual huge bond.
tleap:
tleap -s -f $AMBERHOME/dat/leap/cmd/leaprc.ff14SB
loadamberparams frcmod.ionsjc_tip3p
loadamberparams thioester.frcmod # the modifeid force field file
x = loadpdb "open.pdb"
bond x.160.SG x.76.C # this command was omited while using PDB with
thioester bond.
------------------------------------------------
desc x.160.SG
ATOM
Normal Perturbed
Name: SG SG
Type: S S
Charge: -0.1081 0.000
Polarization: 0.0000 0.000
Element: S (not affected by pert)
Atom flags: (decimal 131072 hex 0x20000)
posfxd n posblt n posdrwn n selected n
pert n notdisp n touched n posknwn Y
internal n needsmin n needsbuild n
Atom position: 52.876000, 16.775000, 28.551000
Atom velocity: 0.000000, 0.000000, 0.000000
Bonded to .R<CYX 160>.A<CB 5> by a single bond.
Bonded to .R<CGLY 76>.A<C 6> by a single bond.
----------------------------------------------------
desc x.76.C
ATOM
Normal Perturbed
Name: C C
Type: C C
Charge: 0.7231 0.000
Polarization: 0.0000 0.000
Element: C (not affected by pert)
Atom flags: (decimal 131072 hex 0x20000)
posfxd n posblt n posdrwn n selected n
pert n notdisp n touched n posknwn Y
internal n needsmin n needsbuild n
Atom position: 54.628000, 16.590000, 28.869000
Atom velocity: 0.000000, 0.000000, 0.000000
Bonded to .R<CGLY 76>.A<CA 3> by a single bond.
Bonded to .R<CGLY 76>.A<O 7> by a single bond.
Bonded to .R<CGLY 76>.A<OXT 8> by a single bond.
Bonded to .R<CYX 160>.A<SG 8> by a single bond.
-----------------------------------------------------
charge x
addions2 x Cl- 0
saveamberparm x prmtop prmcrd
Then the PDB was created using,
ambpdb -p prmtop <prmcrd> check.pdb
This PDB file does not have the "connect" for thioester bond.
I have attached the PDB files herewith.
open.pdb #PDB file without thioester bond
open_with_thioester.pdb # PDB with proteins connected via thioester bond
check.pdb # PDB file obtained from parameter and topology files
Any help is appreciated and thanks in advance!!
---------------------------------------------------------
Aravind R
National Center for biological sciences
Banglore, India
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Received on Wed Apr 11 2018 - 03:00:03 PDT
