[gmx-users] new CHARMM-GUI output not supported?

[Mark Abraham]

On Apr 16, 2013 6:28 AM, "Albert" <mailmd2011 at gmail.com> wrote:
>
> 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?

Maybe. Check out the docs.

>
> 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?

"Support" is not really the right word :-). That force field port and that
builder are things provided by (different?) third parties in the hope that
they are useful. You can't really expect stuff written by three groups of
people at different times to inter-operate seamlessly.

IIRC nbfix has been around for a while,  but I've no idea what it is...

Mark

>  thank you very much
>
> best
> Albert
>
>
>
>
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