Thank you for your answer! I did it and now gromacs throws me the following error: "Atom HG1 in residue SER 2 was not found in rtp entry SER with 11 atoms while sorting atoms.". Any clue? Thank you very much.
Il giorno gio 20 ago 2015 alle ore 13:18 Justin Lemkul <jalem...@vt.edu> ha scritto: > > > On 8/20/15 3:17 AM, Simone Bolognini wrote: > > 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!!! > > > > No, you can't copy and paste, because then you're mixing force fields and > that > is bad practice. HSD is just delta-protonated HIS, which is already in > AMBER. > It's just called HID, so rename your coordinate files appropriately and > you can > generate the topology. > > -Justin > > -- > ================================================== > > Justin A. Lemkul, Ph.D. > Ruth L. Kirschstein NRSA Postdoctoral Fellow > > Department of Pharmaceutical Sciences > School of Pharmacy > Health Sciences Facility II, Room 629 > University of Maryland, Baltimore > 20 Penn St. > Baltimore, MD 21201 > > jalem...@outerbanks.umaryland.edu | (410) 706-7441 > http://mackerell.umaryland.edu/~jalemkul > > ================================================== > -- > 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. > -- 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.