[gmx-users] charmm to gromacs nonbonded parameters after conversion

[ABEL Stephane 175950]

Hi GMX users,
 
I would like to perform MD with new developped CHARMM parameters in GROMACS. Since these parameters are new, they are not presents in the ffcharm*.itp files  given in the of charmm27.ff in the latest GMX distribution. So I have already made the conversions for the bonded parameters. In case of the nonbonded parameters, I have added the LJ values for the new atom types at the end of the  NONBONDED section of a "par_all_27_lipid.prm" file downloaded from the CHARMM website. To convert the LJ values in GROMACS format, I used the perl script of M. Abraham :  convert_charmm_to_gromacs.pl (v.1.3) as follow : 
 
perl convert_charmm_to_gromacs.pl  par_all27_lipid.prm
 
I obtain the ffcharmm.itp and ffcharmmnb.itp files as expected. In the ffcharmmnb.itp the [ atomtypes ] section is present but not the [ pairtypes ] section. Moreover the values in the  [ atomtypes ]  are different compared to same file given in latest GMX distrib (see below). Why these differences ?
----- My ffcharmmnb.itp file 
[ atomtypes ]
;name mass     charge ptype     c6       c12
....
 CTL1 12.011000   0.0     A -0.001485 -6.588e-06 ; -0.000252 -3.793e-07
 CTL2 12.011000   0.0     A -0.001978 -4.173e-06 ; -0.000252 -3.793e-07
 CTL3 12.011000   0.0     A -0.003011 -6.944e-06 ; -0.000252 -3.793e-07
 CTL5 12.011000   0.0     A -0.003274 -8.007e-06 ; -0.000252 -3.793e-07
 CEL1 12.011000   0.0     A -0.003035 -8.095e-06
....
------ GROMACS 4.5.1  ffcharmmnb.itp

[ atomtypes ]
;name at.num mass charge ptype sigma epsilon
....
CTL1 6 12.01100 0.14 A 0.405358916754 0.08368 
CTL2 6 12.01100 0.05 A 0.358141284692 0.234304
CTL3 6 12.01100 -0.27 A 0.363486677001 0.326352 
CTL5 6 12.01100 -0.35 A 0.367050271874 0.33472
CEL1 6 12.01100 -0.15 A 0.372395664183 0.284512 
.....
Thank in advance for your halp 
 
Stefane
 
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