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

[Justin Lemkul]

On 4/16/13 6:50 PM, Mark Abraham wrote:
> 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...
>

It is equivalent to our [ nonbond_params ], if I interpret the documentation 
correctly.

-Justin

-- 
========================================

Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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