[gmx-users] Fatal Error: Unknown bond_atomtype OS. Simulating membrane protein in DPC micelle. PLEASE HELP!!!
Tapash, Arifuzzaman
arifuzz at okstate.edu
Tue Jul 19 10:07:52 CEST 2016
Hi all,
I'm a new user of Gromacs. I have completed the first two tutorials ('Lysozyme in Water' and the 'KALP-15 in DPPC')by Justin Lamkul recently.
Now, I'm trying to simulate a membrane protein (1RKL) in a micelle of DPC. I have collected the DPC micelle (m65.pdb - 65 DPC molecules) from Dr. Tieleman's lab website. I also collected the 'dpc.itp' file from the same website. I'm trying to do this simulation following the 'KALP-15 in DPPC' tutorial.
I have oriented the protein in correct direction and done 'pdb2gmx' on the protein molecule. Then, I modified the gromos force field (ffbonded and ffnonbonded) and the topology (topol.top) file following the tutorial.
I have prepared the DPC topology file (topol_dpc.top) by modifying the 'topol_dppc.top' file provided at that tutorial.
I hope I haven't done any mistake upto that point.
Now, I'm stuck in Step-3 (1. Orient the protein and membrane).
When I was using the grompp command (gmx grompp -f minim.mdp -c m65.gro -p topol_dpc.top -o em.tpr), I am getting an error message saying-
"Unknown bond_atomtype OS"
Then I checked the 'dpc.itp' file, and found that in some places of that file 'OS' atomtype is mentioned, but in the "atomtypes.atp" file in the gromos forcefield, I didn't find any atomtype "OS" defined.
I'm stuck in this stage. How to solve this? Do I have to modify the dpc.itp file or the atomtype.atp file?
Please, HELP!!!
Here I'm attaching the part of the dpc.itp & the atomtype.atp file
##### dpc.itp #####
; topology for a dodecylphosphocholine lipid
[ bondtypes ]
; i j func b0 kb
CH3 NL 1 0.14700 376560.
CH1 OS 1 0.14300 251040.
OS C 1 0.13600 251040.
[ angletypes ]
; i j k func th0 cth
CH3 NL CH3 1 109.500 460.00
CH3 NL CH2 1 109.500 460.00
CH2 CH1 OS 1 109.500 460.00
NL CH2 CH2 1 109.500 460.00
P OS CH2 1 120.000 397.00
OS P OM 1 109.600 397.00
OS P OS 1 103.000 397.00
OM P OM 1 120.000 585.00
OS CH2 CH1 1 111.000 460.00
CH2 CH2 CH1 1 111.000 460.00
CH2 CH2 CH2 1 111.000 460.00
CH2 CH2 CH3 1 111.000 460.00
CH2 CH1 CH2 1 109.500 460.00
CH1 OS C 1 120.000 418.00
CH2 OS C 1 120.000 418.00
CH3 OS C 1 120.000 418.00
OS C O 1 124.000 502.00
OS C CH2 1 115.000 502.00
O C CH2 1 121.000 502.00
C CH2 CH2 1 120.000 585.00
[ moleculetype ]
; Name nrexcl
DPC 3
[ atoms ]
; nr type resnr residu atom cgnr charge mass
1 CH3 1 DPC C1 1 0.4 ; qtot: 0.248
2 CH3 1 DPC C2 1 0.4 ; qtot: 0.496
3 CH3 1 DPC C3 1 0.4 ; qtot: 0.744
4 NL 1 DPC N4 1 -0.5 ; qtot: 0.752
5 CH2 1 DPC C5 1 0.3 ; qtot: 1
6 CH2 1 DPC C6 1 0.4 ; qtot: 1
7 OS 1 DPC O7 1 -0.8 ; qtot: 0.64
8 P 1 DPC P8 1 1.7 ; qtot: 1.64
9 OM 1 DPC O9 1 -0.8 ; qtot: 1
10 OM 1 DPC O10 1 -0.8 ; qtot: 0.36
11 OS 1 DPC O11 1 -0.7 ; qtot: 0
12 CH2 1 DPC C12 5 0 ; qtot: 0
13 CH2 1 DPC C13 6 0 ; qtot: 0
14 CH2 1 DPC C14 7 0 ; qtot: 0
15 CH2 1 DPC C15 8 0 ; qtot: 0
16 CH2 1 DPC C16 9 0 ; qtot: 0
17 CH2 1 DPC C17 10 0 ; qtot: 0
18 CH2 1 DPC C18 11 0 ; qtot: 0
19 CH2 1 DPC C19 12 0 ; qtot: 0
20 CH2 1 DPC C20 13 0 ; qtot: 0
21 CH2 1 DPC C21 14 0 ; qtot: 0
22 CH2 1 DPC C22 15 0 ; qtot: 0
23 CH3 1 DPC C23 16 0 ; qtot: 0
[continued...]
###############################################3
##### atomtype.atp #####
O 15.99940 ; carbonyl oxygen (C=O)
OM 15.99940 ; carboxyl oxygen (CO-)
OA 15.99940 ; hydroxyl, sugar or ester oxygen
OE 15.99940 ; ether or ester oxygen
OW 15.99940 ; water oxygen
N 14.00670 ; peptide nitrogen (N or NH)
NT 14.00670 ; terminal nitrogen (NH2)
NL 14.00670 ; terminal nitrogen (NH3)
NR 14.00670 ; aromatic nitrogen
NZ 14.00670 ; Arg NH (NH2)
NE 14.00670 ; Arg NE (NH)
C 12.01100 ; bare carbon
CH0 12.0110 ; bare sp3 carbon, 4 bound heavy atoms
CH1 13.01900 ; aliphatic or sugar CH-group
CH2 14.02700 ; aliphatic or sugar CH2-group
CH3 15.03500 ; aliphatic CH3-group
CH4 16.04300 ; methane
CH2r 14.02700 ; CH2-group in a ring
CR1 13.01900 ; aromatic CH-group
HC 1.00800 ; hydrogen bound to carbon
H 1.00800 ; hydrogen not bound to carbon
DUM 0.00000 ; dummy atom, no idea what the mass should be. PT3-99
S 32.06000 ; sulfur
CU1+ 63.54600 ; copper (charge 1+)
CU2+ 63.54600 ; copper (charge 2+)
FE 55.84700 ; iron (heme)
ZN2+ 65.37000 ; zinc (charge 2+)
MG2+ 24.30500 ; magnesium (charge 2+)
CA2+ 40.08000 ; calcium (charge 2+)
P 30.97380 ; phosphor
AR 39.94800 ; argon
F 18.99840 ; fluor (non-ionic)
CL 35.45300 ; chlorine (non-ionic)
BR 79.90400 ; bromine (non-ionic)
CMet 15.035 ; CH3-group in methanol (solvent)
OMet 15.9994 ; oxygen in methanol (solvent)
NA+ 22.9898 ; sodium (charge 1+)
CL- 35.45300 ; chlorine (charge 1-)
CChl 12.011 ; carbon in chloroform (solvent)
CLChl 35.453 ; chloride in chloroform (solvent)
HChl 1.008 ; hydrogen in chloroform (solvent)
SDmso 32.06000 ; DMSO Sulphur (solvent)
CDmso 15.03500 ; DMSO Carbon (solvent)
ODmso 15.99940 ; DMSO Oxygen (solvent)
CCl4 12.011 ; carbon in carbontetrachloride (solvent)
CLCl4 35.453 ; chloride in carbontetrachloride (solvent)
FTFE 18.99840 ; fluor in trifluoroethanol
CTFE 12.01100 ; carbon in trifluoroethanol
CHTFE 14.0270 ; CH2-group in trifluoroethanol
OTFE 15.99940 ; oxygen in trifluoroethanol
CUrea 12.01100 ; carbon in urea
OUrea 15.99940 ; oxygen in urea
NUrea 14.00670 ; nitrogen in urea
SI 28.08 ; silicon
MNH3 0 ; Dummy mass in rigid tetraedrical NH3 group
MW 0 ; Dummy mass in rigid tyrosine rings
####################################################
Thanks in advance!!!
[Note: In my last question Dr. Lemkul helped me but I couldn't thank him as I couldn't find a way to reply him. I want to thank all of you who are working hard to develop and improve these software and constantly helping us and each other, a BIG THANKS!!!]
Best,
Arifuzzaman Tapash
More information about the gromacs.org_gmx-users
mailing list