[gmx-users] errors with charmm36 ?

[Albert]

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....

thank you very much.

Albert


On 01/14/2014 02:55 PM, hubert santuz wrote:
> Hi,
>
> I just came across this issue a few days ago (with charmm-gui also).
> In fact, atoms C13, C14 and C15 should be just after the C12 atoms in 
> the pdb (to match the itp file).
>
> Here a piece of code that I used to retrieve the good order for all 
> POPC molecules in your gro file (on unix platform) :
>
> for i in `grep "POPC   C13" yourfile.gro --line-number | awk -F: 
> '{print $1}'`
> do
>     j=$((i-3))
>     (echo "${i}m${j}"; echo w; echo q ) | ed yourfile.gro
> done
>
> Basically, ed is used to move each line "POPC C13", 3 lines above. (6 
> lines for C14 and 9 lines for C15).
>
> Beware also that a  certain number of atom's name are wrong also :
> "0C21" (charmm-gui file) --> 'C210' (itp file)
> "1H10" --> 'H101'
> etc.
> In this case, 'sed' is a great tool ;)
>
> Cheers,
> Hubert