Hello, I am trying to add ethanol as a new residue to CGenFF force field in gromacs. Basically, I need to bring this information from charmm rtf file to the gromacs format. This is the information taken from rtf file of charmm.
RESI ETOH 0.00 ! C2H6O Ethanol, adm jr. GROUP ATOM C1 CG321 0.05 ! H21 H11 H12 ATOM O1 OG311 -0.65 ! \ \ / ATOM HO1 HGP1 0.42 ! H22--C2--C1 ATOM H11 HGA2 0.09 ! / \ ATOM H12 HGA2 0.09 ! H23 O1--HO1 GROUP ATOM C2 CG331 -0.27 ATOM H21 HGA3 0.09 ATOM H22 HGA3 0.09 ATOM H23 HGA3 0.09 BOND C1 C2 C1 O1 C1 H11 C1 H12 O1 HO1 BOND C2 H21 C2 H22 C2 H23 DONO HO1 O1 ACCE O1 ! for ic build IC O1 C1 C2 H21 0.0000 0.0000 180.0000 0.0000 0.0000 IC C1 H21 *C2 H22 0.0000 0.0000 120.0000 0.0000 0.0000 IC C1 H21 *C2 H23 0.0000 0.0000 240.0000 0.0000 0.0000 IC O1 C2 *C1 H11 0.0000 0.0000 240.0000 0.0000 0.0000 IC O1 C2 *C1 H12 0.0000 0.0000 120.0000 0.0000 0.0000 IC C2 C1 O1 HO1 0.0000 0.0000 180.0000 0.0000 0.0000 I have added The ATOM and BOND information to the aminoacid.rtp file. I thought that the rest of the information are optional and pdb2gmx doesn't complain while generating the topology. But when I use the topology and gro file to do a minimization. The molecule bonds break apart and what I see is an exploded molecule. So I thought probably the rest of the information are important too, for example: DONO HO1 O1 ACCE O1 But I dont know where to put them. Thanks G. -- 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
