On Mon, Nov 9, 2009 at 8:35 PM, Justin A. Lemkul <jalem...@vt.edu> wrote: > > > Jack Shultz wrote: > > <snip> > >> ------------------------------------------------------- >> Program pdb2gmx, VERSION 4.0.5 >> Source code file: pdb2gmx.c, line: 429 >> >> Fatal error: >> Atom O in residue CARG 244 not found in rtp entry with 25 atoms >> while sorting atoms >> ------------------------------------------------------- >> >> But we got an O here >> ATOM 3822 O CARG 153 -4.455 -21.080 2.791 1.00 0.00 >> O >> > > The error is not telling you that the O atom is missing from the .pdb file; > it is telling you that it is present in the .pdb, but not in the .rtp entry. > Look at the .rtp entry for CARG
[ CARG ] [ atoms ] N amber99_34 -0.34810 1 H amber99_17 0.27640 2 CA amber99_11 -0.30680 3 HA amber99_19 0.14470 4 CB amber99_11 -0.03740 5 HB1 amber99_18 0.03710 6 HB2 amber99_18 0.03710 7 CG amber99_11 0.07440 8 HG1 amber99_18 0.01850 9 HG2 amber99_18 0.01850 10 CD amber99_11 0.11140 11 HD1 amber99_19 0.04680 12 HD2 amber99_19 0.04680 13 NE amber99_38 -0.55640 14 HE amber99_17 0.34790 15 CZ amber99_3 0.83680 16 NH1 amber99_38 -0.87370 17 HH11 amber99_17 0.44930 18 HH12 amber99_17 0.44930 19 NH2 amber99_38 -0.87370 20 HH21 amber99_17 0.44930 21 HH22 amber99_17 0.44930 22 C amber99_2 0.85570 23 OC1 amber99_45 -0.82660 24 OC2 amber99_45 -0.82660 25 - you should have an O1 and O2 atom for the I made the following modification ATOM 1900 O1 CARG 153 -17.391 -20.267 11.508 1.00 0.00 O ATOM 1909 O2 CARG 153 -18.666 -19.390 13.107 1.00 0.00 O ------------------------------------------------------- Program pdb2gmx, VERSION 4.0.5 Source code file: pdb2gmx.c, line: 429 Fatal error: Atom O in residue CARG 122 not found in rtp entry with 25 atoms while sorting atoms ------------------------------------------------------- > C-terminal carboxylate. > > -Justin > > -- > ======================================== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > -- > gmx-users mailing list gmx-us...@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php > -- Jack http://drugdiscoveryathome.com http://hydrogenathome.org -- 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/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/mailing_lists/users.php