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 ---------------------------- -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
