Thanks Justin! Got it now. On Mon, Nov 9, 2009 at 10:00 PM, Justin A. Lemkul <[email protected]> wrote: > > > Jack Shultz wrote: >> >> On Mon, Nov 9, 2009 at 8:35 PM, Justin A. Lemkul <[email protected]> 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 >> > > Forgive my typo, what I meant was OC1 and OC2. You must always make sure > the atoms in the structure file match those expected by the .rtp file. You > need OC1 and OC2. > > -Justin > >> >> ------------------------------------------------------- >> 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 [email protected] >>> 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 [email protected]. >>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >>> >> >> >> > > -- > ======================================== > > 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 [email protected] > 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 [email protected]. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php >
-- Jack http://drugdiscoveryathome.com http://hydrogenathome.org -- gmx-users mailing list [email protected] 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 [email protected]. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
