[gmx-users] errors with charmm36 ?

[Justin Lemkul]

On 1/14/14, 10:09 AM, Albert wrote:
> Hi Justin and Hubert:
>
> Many thanks for your kind pointing out. Are you using the new version of
> CHARMM36? I am using the one from here:
>
> http://mackerell.umaryland.edu/download.php?filename=CHARMM_ff_params_files/charmm36_gmx_format_sep13.tgz
>
>
> I opened the merged.rtp file within the charmm36.ff file and found:
>
> [ POPC ]
>    [ atoms ]
>          N   NTL   -0.600  0
>        C12  CTL2   -0.100  1
>       H12A    HL    0.250  2
>       H12B    HL    0.250  3
>        C13  CTL5   -0.350  4
>       H13A    HL    0.250  5
>       H13B    HL    0.250  6
>       H13C    HL    0.250  7
>        C14  CTL5   -0.350  8
>       H14A    HL    0.250  9
>       H14B    HL    0.250 10
>       H14C    HL    0.250 11
>        C15  CTL5   -0.350 12
>       H15A    HL    0.250 13
>       H15B    HL    0.250 14
>       H15C    HL    0.250 15
>        C11  CTL2   -0.080 16
>       H11A  HAL2    0.090 17
>       H11B  HAL2    0.090 18
>          P    PL    1.500 19
>        O13   O2L   -0.780 20
>
> Here is the information in my system.pdb file:
>
> CRYST1   68.504   68.504  100.000  90.00  90.00  90.00 P 1           1
> ATOM      1  N   POPCA   1     -23.882  12.660  22.550 1.00-19.80      MEMB
> ATOM      2  C12 POPCA   1     -23.575  13.505  21.320 1.00-19.52      MEMB
> ATOM      3 H12A POPCA   1     -22.869  12.963  20.709  1.00 0.00      MEMB
> ATOM      4 H12B POPCA   1     -23.032  14.387  21.628  1.00 0.00      MEMB
> ATOM      5  C13 POPCA   1     -24.769  11.520  22.190 1.00-20.41      MEMB
> ATOM      6 H13A POPCA   1     -24.241  10.891  21.490  1.00 0.00      MEMB
> ATOM      7 H13B POPCA   1     -25.124  11.119  23.128  1.00 0.00      MEMB
> ATOM      8 H13C POPCA   1     -25.638  11.934  21.700  1.00 0.00      MEMB
> ATOM      9  C14 POPCA   1     -22.673  12.210  23.289 1.00-19.18      MEMB
> ATOM     10 H14A POPCA   1     -23.025  11.888  24.257  1.00 0.00      MEMB
> ATOM     11 H14B POPCA   1     -22.117  11.419  22.806  1.00 0.00      MEMB
> ATOM     12 H14C POPCA   1     -21.935  12.981  23.456  1.00 0.00      MEMB
> ATOM     13  C15 POPCA   1     -24.601  13.537  23.461 1.00-18.70      MEMB
> ATOM     14 H15A POPCA   1     -24.979  13.080  24.364  1.00 0.00      MEMB
> ATOM     15 H15B POPCA   1     -25.469  13.977  22.992  1.00 0.00      MEMB
> ATOM     16 H15C POPCA   1     -23.953  14.351  23.749  1.00 0.00      MEMB
> ATOM     17  C11 POPCA   1     -24.755  13.765  20.262 1.00-20.80      MEMB
> ATOM     18 H11A POPCA   1     -24.458  14.498  19.482  1.00 0.00      MEMB
> ATOM     19 H11B POPCA   1     -25.669  14.146  20.766  1.00 0.00      MEMB
> ATOM     20  P   POPCA   1     -24.213  11.984  18.366 1.00-18.20      MEMB
> ATOM     21  O13 POPCA   1     -24.848  10.757  17.832 1.00-17.27      MEMB
> ATOM     22  O14 POPCA   1     -22.825  11.910  18.814 1.00-18.67      MEMB
> ATOM     23  O12 POPCA   1     -25.078  12.575  19.526 1.00-17.51      MEMB
>
> The line 3 in merged.rtp and my .pdb file are H12a. The order seems to be all
> right....
>

The .top is what matters, and your topology showed a clearly different order of 
atoms.  Check the correspondence of the output configuration from pdb2gmx and 
the .top file.  Inputs and .rtp entries are irrelevant once pdb2gmx is done working.

-Justin

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

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441

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