Hi everyone, I have a .pdb file of the WW domain of human FIP35 protein extracted from an MD calculation obtained with AMBER ff99SB-ILDN and solvent type tip3. Now I need to obtain the topology out of it, but the .pdb contains a residue, namely HSD, which is not present in the Amber residue database. I looked at the source files and found out that CHARMM has it. In particular, this is what you can find in the CHARMM database:
[ HSD ] [ atoms ] N NH1 -0.47 0 HN H 0.31 1 CA CT1 0.07 2 HA HB 0.09 3 CB CT2 -0.09 4 HB1 HA 0.09 5 HB2 HA 0.09 6 ND1 NR1 -0.36 7 HD1 H 0.32 8 CG CPH1 -0.05 9 CE1 CPH2 0.25 10 HE1 HR1 0.13 11 NE2 NR2 -0.70 12 CD2 CPH1 0.22 13 HD2 HR3 0.10 14 C C 0.51 15 O O -0.51 16 [ bonds ] CB CA CG CB ND1 CG CE1 ND1 NE2 CD2 N HN N CA C CA C +N CA HA CB HB1 CB HB2 ND1 HD1 CD2 HD2 CE1 HE1 O C CG CD2 CE1 NE2 [ impropers ] ND1 CG CE1 HD1 CD2 CG NE2 HD2 CE1 ND1 NE2 HE1 ND1 CE1 CG HD1 CD2 NE2 CG HD2 CE1 NE2 ND1 HE1 N -C CA HN C CA +N O [ cmap ] -C N CA C +N Is there any possible way in which I can "copy and paste" this in the Amber database and hope it will work correctly? Thank you very much!!! -- 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.