I don't know. Parachem outputs stuff like this (CHARMM toppar format):
(propionic acid, C3H2O5) RESI PROA -1.00 GROUP ATOM C2 CG321 -0.28 ATOM C1 CG2O3 0.62 ATOM H21 HGA2 0.09 ATOM H22 HGA2 0.09 ATOM O1 OG2D2 -0.76 ATOM O2 OG2D2 -0.76 GROUP ATOM C3 CG331 -0.27 ATOM H31 HGA3 0.09 ATOM H32 HGA3 0.09 ATOM H33 HGA3 0.09 BOND C1 C2 C2 C3 C1 O1 BOND C2 H21 C2 H22 BOND C3 H31 C3 H32 C3 H33 DOUBLE C1 O2 IMPR C1 O2 O1 C2 which you can easily write a script to convert to .rtp (or just convert by hand) but it'd be more complicated to create an entire .itp from this format; pdb2gmx will do it if you convert this to .rtp though. I also frequently encounter ligands that don't have hydrogens too, so that's why I would write a .hdb entry if necessary. (As a side note, Gromacs shouldn't use charge groups when using all-atom charmm forcefields.) On 2012-12-20 09:27:12AM +0100, Albert wrote: > On 12/20/2012 09:13 AM, pcl wrote: > > Well what works for me is I convert cgenff and merge it with charmm36 (you > > only have to do this once per cgenff version), then I have paramchem > > generate cgenff charges for the ligand. Then I convert the output of > > paramchem (charges) to .rtp format. I also have to create .hdb entries. > > Paramchem may also generate additional cgenff atom interactions (dihedrals > > or impropers) that may not exist by default, I usually convert and add > > those to forcefield's .itp files. Then pdb2gmx will work on the ligand pdb. > > > but isn't there is a script to do so in Gromacs webiste, which can > convert the output from parachem into Gromacs .itp format? although I > didn't try it hard, because I don't find any documentation to use it > correctly..... > -- > gmx-users mailing list [email protected] > 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 [email protected]. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- -- gmx-users mailing list [email protected] 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 [email protected]. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
