[gmx-users] Charge groups in Charmm for lipids

[Michael McGovern]

Thanks a lot, I will check that out.


________________________________
From: Thomas Piggot <t.piggot at soton.ac.uk>
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Sent: Friday, August 5, 2011 6:48 PM
Subject: Re: [gmx-users] Charge groups in Charmm for lipids


 Hi,

Yes, this was done on purpose to reflect the different use of charge
    groups in CHARMM and GROMACS. Check out the mailing list archives
    for more details about this. 

On another note you might like to take a look at the contributed
    CHARMM36 force field (available to download on the GROMACS website).
    There is a DPPG entry in the lipids.rtp file that should help in
    making a CHARMM27 DPPG rtp entry (if you wish to use the CHARMM27
    lipids rather than the CHARMM36 ones).

Cheers

Tom 

On 06/08/11 00:22, Michael McGovern wrote: 
Hi, I'm making a lipid topology for DPPG in the charmm forcefield in gromacs 4.5.  I'm putting it together from pieces of what already exists as suggested in the charmm files.  I noticed that there are charge groups in the original charmm files, and these were reflected in the gromacs topology in the 4.5 beta release, but in 4.5.3 and 4.5.4, every atom has its own charge group.  
>
>
>So for instace, POPC in the beta release had a topology that began:
>[ POPC ]
> [ atoms ]
>        N       NTL     -0.60   0
>        C11     CTL2    -0.10   0
>        C12     CTL5    -0.35   0
>        C13     CTL5    -0.35   0
>        C14     CTL5    -0.35   0
>        H11     HL      0.25    0
>        H12     HL      0.25    0
>        H21     HL      0.25    0
>        H22     HL      0.25    0
>        H23     HL      0.25    0
>        H31     HL      0.25    0
>        H32     HL      0.25    0
>        H33     HL      0.25    0
>        H41     HL      0.25    0
>        H42     HL      0.25    0
>        H43     HL      0.25    0
>        C15     CTL2    -0.08   1
>        H51     HAL2    0.09    1
>        H52     HAL2    0.09    1
>        P1      PL      1.50    2
>        O3      O2L     -0.78   2
>        O4      O2L     -0.78   2
>        O1      OSL     -0.57   2
>        O2      OSL     -0.57   2
>        C1      CTL2    -0.08   3
>...
>While in 4.5.4 this is
>[ POPC ]
> [ atoms ]
>        N       NTL     -0.60   0
>        C11     CTL2    -0.10   1
>        C12     CTL5    -0.35   2
>        C13     CTL5    -0.35   3
>        C14     CTL5    -0.35   4
>        H11     HL      0.25    5
>        H12     HL      0.25    6
>        H21     HL      0.25    7
>        H22     HL      0.25    8
>        H23     HL      0.25    9
>        H31     HL      0.25    10
>        H32     HL      0.25    11
>        H33     HL      0.25    12
>        H41     HL      0.25    13
>        H42     HL      0.25    14
>        H43     HL      0.25    15
>        C15     CTL2    -0.08   16
>        H51     HAL2    0.09    17
>...
>The charge groups do not have integer charge and are all one atom.  The beta version has groups that agree with the charmm groups and have integer charge.  Was this changed on purpose? The beta version seems correct to me, but am I missing something as to why this change would be made?  
>Thanks

-- 
Dr Thomas Piggot
University of Southampton, UK. 
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