Hi I have three water molecules and one new residue that I want to add their parameters to force field Amber99sb. One of water molecules has only one hydrogen, and since I want to prevent from replacing with SOL in solvation step, So I define them as new residue in .rtp file:
[ INN ] [ atoms ] H1 H 0.384620 1 O O -0.671930 2 H2 H 0.384620 3 [ INT ] [ atoms ] H1 H 0.286310 1 O O -0.341910 2 H2 H 0.286310 3 [ INB ] [ atoms ] H1 H 0.477860 1 O O -1.092580 2 Also define them in .dat file as Protein and in .hdb file as below: INN 2 1 7 H1 O 1 7 H2 O INT 2 1 7 H1 O 1 7 H2 O INB 1 1 7 H1 O But when I start MD simulation(gromacs 5.0.4) in step of mdrun ...em, gives segmentation fault! when I remove their parameters in .hdb file, it is done but without any hydrogen for them, just three oxygen atoms in em.gro! Also I have another problem with that new residue, this residue is like a Lys but has two carbonyl groups binded to extra carbon instead of amino group in Lys. So I used Lys parameters for that and add some bonds and atoms to it: [ NEW ] ; [ atoms ] N N H H CA CT HA H1 CB CT HB1 HC HB2 HC CG CT HG1 H HG2 H CD CT HD1 HC HD2 HC CE CT HE1 HP HE2 HP NZ N HZ H CX C OQ1 O OQ2 O C C O O [ bonds ] N H N CA CA HA CA CB CA C CB HB1 CB HB2 CB CG CG HG1 CG HG2 CG CD CD HD1 CD HD2 CD CE CE HE1 CE HE2 CE NZ NZ HZ NZ CX C O CX OQ1 CX OQ2 [ impropers ] -C CA N H CA +N C O when I added only atoms parameters in .rtp file, finally in em.gro file there wasn't any bond between atoms of new residue and when I added bond parameters also, in grompp gives 10 error about "default angel and dihedral"! I find the number of angels in .top file and added them to ffbonded.itp, but anything have no change. please help me. what is my mistake about these two insistent problems? Thanks Malihe -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.