[gmx-users] Re: berger-oplsaa combination for DPC micelle
Low Soo Mei
lowsm at bii.a-star.edu.sg
Wed Jun 4 20:42:58 CEST 2008
Hi,
Thank you Chris for the helpful answer! I have modified the atomtype
names to follow dmpc.itp, which is more familiar to me, but those names
are also the same as popc.itp. There is probably something wrong with
the way I did it because although the "atomtype not found" errors have
stopped, I am getting "no default bond types (lines 68-86) / angle types
(lines 138, 147) / proper dihedral types (lines 161-167)". My modified
dpc_double_pairlist.itp file is attached below.
> Message: 7
> Date: Wed, 04 Jun 2008 12:01:33 -0400
> From: chris.neale at utoronto.ca
> Subject: [gmx-users] berger-oplsaa combination for DPC micelle
> To: gmx-users at gromacs.org
> Message-ID: <20080604120133.htonx5kcw8gg8c48 at webmail.utoronto.ca>
> Content-Type: text/plain; charset=ISO-8859-1; DelSp="Yes";
> format="flowed"
>
> In general, you should always post your relevant files with your
> question. It makes it easier for us to answer you. That said, I happen
> to have already used DPC and here is what I have done. I made a new
> dpc_rename.itp and it is quite different, but should simulate the
> exact same. Here is the beginning of the atoms section
>
> ;Chris Neale modified atomtype names here to follow popc.itp
> ; Atoms double checked vs. popc.itp by CN Oct5 2006
> [ atoms ]
> ; nr type resnr residu atom cgnr charge mass
> 1 LC3 1 DPC C1 1 0.4 ; qtot: 0.248
> 2 LC3 1 DPC C2 1 0.4 ; qtot: 0.496
> 3 LC3 1 DPC C3 1 0.4 ; qtot: 0.744
> 4 LNL 1 DPC N4 1 -0.5 ; qtot: 0.752
> 5 LH2 1 DPC C5 1 0.3 ; qtot: 1
>
> and then you need to make modifications to the other sections so that
> the parameters are found appropriately.
>
> Chris.
>
> -- original message --
>
> Hi Gromacs users,
>
> I am trying to simulate a protein with a micelle, and have used dpc.itp
> from Dr. Tieleman's site. I have also introduced parts of lipid.itp
> into ffoplsaanb.itp and ffoplsaabon.itp in accordance with Chris Neale's
> half-epsilon double-pairlist method. But when I issue a grompp command
> for minimization, grompp gives a fatal error that the "Bonded/nonbonded
> atom type 'CH3' not found!". This atom type CH3 is present in dpc.itp.
> I am now wondering if I can match this to some existing atom in the
> oplsaa and how I might go about choosing which atom.
>
> I would be grateful for your advice, and am happy to attach files if needed.
>
> Cheers,
> Soo Mei
>
>
; topology for a dodecylphosphocholine lipid from Tieleman's site.
; modified to follow the other pc.itp's on Tieleman's site, as suggested
by Chris Neale on gmx-users list on 4th June 2008, when I had "atomtype
not found" problems
[ bondtypes ]
; i j func b0 kb
LC3 LNL 1 0.14700 376560. ; formerly CH3 and NL.
; CH1 OS 1 0.14300 251040. ; no CH1 in DPC.
; OS C 1 0.13600 251040. ; no C in DPC. C is the
ester-linkage carbon that joins the glycerol backbone to the long lipid
chains in the pc.itp's.
[ angletypes ]
; i j k func th0 cth
LC3 LNL LC3 1 109.500 460.00 ; formerly CH3 NL CH3
LC3 LNL LH2 1 109.500 460.00 ; formerly CH3 NL CH2
; CH2 CH1 OS 1 109.500 460.00 ; no CH1 in DPC.
LNL LH2 LC2 1 109.500 460.00 ; formerly NL CH2 CH2
LP LOS LC2 1 120.000 397.00 ; formerly P OS CH2. Can't
decide if it's 8 7 6 or 8 11 12. Will put for both. This is 8 7 6
LP LOS LP2 1 120.000 397.00 ; and this is 8 11 12.
LOS LP LOM 1 109.600 397.00 ; formerly OS P OM
LOS LP LOS 1 103.000 397.00 ; formerly OS P OS
LOM LP LOM 1 120.000 585.00 ; formerly OM P OM
; OS CH2 CH1 1 111.000 460.00 ; no CH1 in DPC.
; CH2 CH2 CH1 1 111.000 460.00 ; no CH1 in DPC.
LP2 LP2 LP2 1 111.000 460.00
LP2 LP2 LP3 1 111.000 460.00
; CH2 CH1 CH2 1 109.500 460.00 ; no CH1 in DPC.
; CH1 OS C 1 120.000 418.00 ; no CH1 or C in DPC.
; CH2 OS C 1 120.000 418.00 ; no C in DPC.
; CH3 OS C 1 120.000 418.00 ; no C in DPC.
; OS C O 1 124.000 502.00 ; no C in DPC.
; OS C CH2 1 115.000 502.00 ; no C in DPC.
; O C CH2 1 121.000 502.00 ; no C in DPC.
; C CH2 CH2 1 120.000 585.00 ; no C in DPC.
[ moleculetype ]
; Name nrexcl
DPC 3
[ atoms ]
; nr type resnr residu atom cgnr charge mass
1 LC3 1 DPC C1 1 0.4 ; qtot:
0.248, type formerly CH3
2 LC3 1 DPC C2 1 0.4 ; qtot:
0.496, type formerly CH3
3 LC3 1 DPC C3 1 0.4 ; qtot:
0.744, type formerly CH3
4 LNL 1 DPC N4 1 -0.5 ; qtot:
0.752, type formerly NL
5 LH2 1 DPC C5 1 0.3 ; qtot:
1, type formerly CH2
6 LC2 1 DPC C6 1 0.4 ; qtot:
1, type formerly CH2
7 LOS 1 DPC O7 1 -0.8 ; qtot:
0.64, type formerly OS
8 LP 1 DPC P8 1 1.7 ; qtot:
1.64, type formerly P
9 LOM 1 DPC O9 1 -0.8 ; qtot:
1, type formerly OM
10 LOM 1 DPC O10 1 -0.8 ; qtot:
0.36, type formerly OM
11 LOS 1 DPC O11 1 -0.7 ; qtot:
0, type formerly OS
12 LP2 1 DPC C12 5 0 ; qtot:
0, type formerly CH2
13 LP2 1 DPC C13 6 0 ; qtot:
0, type formerly CH2
14 LP2 1 DPC C14 7 0 ; qtot:
0, type formerly CH2
15 LP2 1 DPC C15 8 0 ; qtot:
0, type formerly CH2
16 LP2 1 DPC C16 9 0 ; qtot:
0, type formerly CH2
17 LP2 1 DPC C17 10 0 ; qtot:
0, type formerly CH2
18 LP2 1 DPC C18 11 0 ; qtot:
0, type formerly CH2
19 LP2 1 DPC C19 12 0 ; qtot:
0, type formerly CH2
20 LP2 1 DPC C20 13 0 ; qtot:
0, type formerly CH2
21 LP2 1 DPC C21 14 0 ; qtot:
0, type formerly CH2
22 LP2 1 DPC C22 15 0 ; qtot:
0, type formerly CH2
23 LP3 1 DPC C23 16 0 ; qtot:
0, type formerly CH3
[ bonds ]
; ai aj funct
1 4 1
2 4 1
3 4 1
4 5 1
5 6 1
6 7 1
7 8 1
8 9 1
8 10 1
8 11 1
11 12 1
12 13 1
13 14 1
14 15 1
15 16 1
16 17 1
17 18 1
18 19 1
19 20 1
20 21 1
21 22 1
22 23 1
[ pairs ]
; ai aj funct
; Here is the first copy.
1 6 1
2 6 1
3 6 1
4 7 1
5 8 1
6 9 1
6 10 1
6 11 1
7 12 1
8 13 1
9 12 1
10 12 1
11 14 1
; 12 15 1
; 13 16 1
; 14 17 1
; 15 18 1
; 16 19 1
; 17 20 1
; 18 21 1
; 19 22 1
; 20 23 1
; Here is the second copy. Only use this with the halved LJ-14 epsilon
values.
1 6 1
2 6 1
3 6 1
4 7 1
5 8 1
6 9 1
6 10 1
6 11 1
7 12 1
8 13 1
9 12 1
10 12 1
11 14 1
[ angles ]
; ai aj ak funct
1 4 2 1
1 4 3 1
1 4 5 1
2 4 3 1
2 4 5 1
3 4 5 1
4 5 6 1
5 6 7 1
6 7 8 1
7 8 9 1
7 8 10 1
7 8 11 1
9 8 10 1
9 8 11 1
10 8 11 1
8 11 12 1
11 12 13 1
12 13 14 1
13 14 15 1
14 15 16 1
15 16 17 1
16 17 18 1
17 18 19 1
18 19 20 1
19 20 21 1
20 21 22 1
21 22 23 1
[ dihedrals ]
; ai aj ak al funct
1 4 5 6 1
4 5 6 7 1
5 6 7 8 1
6 7 8 9 1
7 8 11 12 1
8 11 12 13 1
11 12 13 14 1
12 13 14 15 3
13 14 15 16 3
14 15 16 17 3
15 16 17 18 3
16 17 18 19 3
17 18 19 20 3
18 19 20 21 3
19 20 21 22 3
20 21 22 23 3
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