Hello:
I obtained a POPC lipids from CHARMM-GUI and I found the initial 12
line are following:
following atom name order:
ATOM 6315 N POPC 22 3.580 -22.614 19.970 1.00-19.29 MEMB
ATOM 6316 C12 POPC 22 4.563 -22.414 18.821 1.00-17.85 MEMB
ATOM 6317 H12A POPC 22 4.337 -21.455 18.379 1.00 0.00 MEMB
ATOM 6318 H12B POPC 22 5.583 -22.427 19.173 1.00 0.00 MEMB
ATOM 6319 C13 POPC 22 3.979 -23.730 20.844 1.00-17.96 MEMB
ATOM 6320 H13A POPC 22 3.969 -24.679 20.329 1.00 0.00 MEMB
ATOM 6321 H13B POPC 22 4.977 -23.582 21.229 1.00 0.00 MEMB
ATOM 6322 H13C POPC 22 3.420 -23.829 21.763 1.00 0.00 MEMB
ATOM 6323 C14 POPC 22 3.424 -21.320 20.778 1.00-20.44 MEMB
ATOM 6324 H14A POPC 22 2.552 -21.497 21.391 1.00 0.00 MEMB
ATOM 6325 H14B POPC 22 4.281 -21.118 21.404 1.00 0.00 MEMB
ATOM 6326 H14C POPC 22 3.249 -20.474 20.130 1.00 0.00 MEMB
And here is initial 12 line Slipid popc.itp:
; residue 1 POPC rtp POPC q 0.0
1 NTL 1 POPC N 1 -0.6 14.007 ; qtot
-0.6
2 CTL2 1 POPC C12 2 -0.1 12.011 ; qtot
-0.7
3 CTL5 1 POPC C13 3 -0.35 12.011 ; qtot
-1.05
4 CTL5 1 POPC C14 4 -0.35 12.011 ; qtot
-1.4
5 CTL5 1 POPC C15 5 -0.35 12.011 ; qtot
-1.75
6 HL 1 POPC H12A 6 0.25 1.008 ; qtot
-1.5
7 HL 1 POPC H12B 7 0.25 1.008 ; qtot
-1.25
8 HL 1 POPC H13A 8 0.25 1.008 ; qtot -1
9 HL 1 POPC H13B 9 0.25 1.008 ; qtot
-0.75
10 HL 1 POPC H13C 10 0.25 1.008 ; qtot
-0.5
11 HL 1 POPC H14A 11 0.25 1.008 ; qtot
-0.25
12 HL 1 POPC H14B 12 0.25 1.008 ; qtot 0
And here is initial 12 line in CHARMM36.ff/lipids.rtp file:
[ POPC ]
[ atoms ]
N NTL -0.60 0
C12 CTL2 -0.10 1
C13 CTL5 -0.35 2
C14 CTL5 -0.35 3
C15 CTL5 -0.35 4
H12A HL 0.25 5
H12B HL 0.25 6
H13A HL 0.25 7
H13B HL 0.25 8
H13C HL 0.25 9
H14A HL 0.25 10
H14B HL 0.25 11
As we can see the Slipids popc.itp is the same with CHARMM36.ff/lipids.rtp
, but both of which are different from current CHARMM-GUI output.
Probably CHARMM-GUI
change its format, and Slipids FF and CHARMM36 FF in Gromacs cannot
support current new version
CHARMM-GUI output?
Moreover, the new CHARMM36 FF (both for protein, lipids and
ions)introduced Residue pair specific (native contact) non-bonded
parameters, nbfix term,
probably it is also not supported in current CHARMM36FF in Gromacs?
thank you very much
best
Albert
--- Begin Message ---
Hello:
I obtained a POPC lipids from CHARMM-GUI and I found the initial 12 line are
following:
following atom name order:
ATOM 6315 N POPC 22 3.580 -22.614 19.970 1.00-19.29 MEMB
ATOM 6316 C12 POPC 22 4.563 -22.414 18.821 1.00-17.85 MEMB
ATOM 6317 H12A POPC 22 4.337 -21.455 18.379 1.00 0.00 MEMB
ATOM 6318 H12B POPC 22 5.583 -22.427 19.173 1.00 0.00 MEMB
ATOM 6319 C13 POPC 22 3.979 -23.730 20.844 1.00-17.96 MEMB
ATOM 6320 H13A POPC 22 3.969 -24.679 20.329 1.00 0.00 MEMB
ATOM 6321 H13B POPC 22 4.977 -23.582 21.229 1.00 0.00 MEMB
ATOM 6322 H13C POPC 22 3.420 -23.829 21.763 1.00 0.00 MEMB
ATOM 6323 C14 POPC 22 3.424 -21.320 20.778 1.00-20.44 MEMB
ATOM 6324 H14A POPC 22 2.552 -21.497 21.391 1.00 0.00 MEMB
ATOM 6325 H14B POPC 22 4.281 -21.118 21.404 1.00 0.00 MEMB
ATOM 6326 H14C POPC 22 3.249 -20.474 20.130 1.00 0.00 MEMB
And here is initial 12 line Slipid popc.itp:
; residue 1 POPC rtp POPC q 0.0
1 NTL 1 POPC N 1 -0.6 14.007 ; qtot -0.6
2 CTL2 1 POPC C12 2 -0.1 12.011 ; qtot -0.7
3 CTL5 1 POPC C13 3 -0.35 12.011 ; qtot -1.05
4 CTL5 1 POPC C14 4 -0.35 12.011 ; qtot -1.4
5 CTL5 1 POPC C15 5 -0.35 12.011 ; qtot -1.75
6 HL 1 POPC H12A 6 0.25 1.008 ; qtot -1.5
7 HL 1 POPC H12B 7 0.25 1.008 ; qtot -1.25
8 HL 1 POPC H13A 8 0.25 1.008 ; qtot -1
9 HL 1 POPC H13B 9 0.25 1.008 ; qtot -0.75
10 HL 1 POPC H13C 10 0.25 1.008 ; qtot -0.5
11 HL 1 POPC H14A 11 0.25 1.008 ; qtot -0.25
12 HL 1 POPC H14B 12 0.25 1.008 ; qtot 0
And here is initial 12 line in CHARMM36.ff/lipids.rtp file:
[ POPC ]
[ atoms ]
N NTL -0.60 0
C12 CTL2 -0.10 1
C13 CTL5 -0.35 2
C14 CTL5 -0.35 3
C15 CTL5 -0.35 4
H12A HL 0.25 5
H12B HL 0.25 6
H13A HL 0.25 7
H13B HL 0.25 8
H13C HL 0.25 9
H14A HL 0.25 10
H14B HL 0.25 11
As we can see the Slipids popc.itp is the same with CHARMM36.ff/lipids.rtp
, but both of which are different from current CHARMM-GUI output. Probably
CHARMM-GUI
change its format, and Slipids FF and CHARMM36 FF in Gromacs cannot support
current new version
CHARMM-GUI output?
Moreover, the new CHARMM36 FF (both for protein, lipids and ions)introduced
Residue pair specific (native contact) non-bonded parameters, nbfix term,
probably it is also not supported in current CHARMM36FF in Gromacs?
thank you very much
best
Shuguang
--- End Message ---
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