Problem is solved. The atom needed to be called O not O2. Thanks, On Tue, Sep 15, 2009 at 11:29 PM, Justin A. Lemkul <jalem...@vt.edu> wrote:
> > > Gunnar Widtfeldt Reginsson wrote: > >> Hi. Can someone please help me. >> >> I am new to Gromacs. I have a 20mer DNA duplex I want to do some MD on. I >> start by making a topology file form the pdb file. When I run pdb2gmx and >> the amber99 force field I get this fatal error: >> 'Atom 02 in residue DT 3 not found in rtp entry with 32 atoms while >> sorting atoms' >> >> Here is the portion of the pdb file containing the atom in question: >> ATOM 37 C4 DA A 2 2.705 -1.868 3.118 1.00 0.00 >> ATOM 38 C3' DA A 2 6.858 -4.420 2.715 1.00 0.00 >> ATOM 39 C2' DA A 2 5.664 -4.141 3.627 1.00 0.00 >> ATOM 40 O3' DA A 2 7.933 -3.562 3.073 1.00 0.00 >> ATOM 41 P DT A 3 8.308 -3.390 4.619 1.00 0.00 >> ATOM 42 O1P DT A 3 9.773 -3.228 4.760 1.00 0.00 >> ATOM 43 O2P DT A 3 7.705 -4.493 5.401 1.00 0.00 >> ATOM 44 O5' DT A 3 7.575 -2.013 4.972 1.00 0.00 >> ATOM 45 C5' DT A 3 7.588 -0.948 4.004 1.00 0.00 >> Where atom 02 must be O1P in DT 3 >> >> > I don't know how you reach the conclusion that pdb2gmx is confusing atom 02 > (which by the way is a "zero"-2 in the error message, not an "oh", if you > have copied and pasted directly) with atom O1P. > > It could be a problem of formatting (incorrect spacing), or somewhere else > in the residue you have an atom labeled 02 (with a zero). > > -Justin > > Here is the portion of the amber99 .rtf file for the DT nucleotide: >> [ DT ] >> [ atoms ] >> P amber99_46 1.16590 1 >> O1P amber99_45 -0.77610 2 >> O2P amber99_45 -0.77610 3 >> O5' amber99_44 -0.49540 4 >> C5' amber99_11 -0.00690 5 >> H5'1 amber99_19 0.07540 6 >> H5'2 amber99_19 0.07540 7 >> C4' amber99_11 0.16290 8 >> H4' amber99_19 0.11760 9 >> O4' amber99_44 -0.36910 10 >> C1' amber99_11 0.06800 11 >> H1' amber99_20 0.18040 12 >> N1 amber99_40 -0.02390 13 >> C6 amber99_7 -0.22090 14 >> H6 amber99_23 0.26070 15 >> C5 amber99_7 0.00250 16 >> C7 amber99_11 -0.22690 17 >> H71 amber99_18 0.07700 18 >> H72 amber99_18 0.07700 19 >> H73 amber99_18 0.07700 20 >> C4 amber99_2 0.51940 21 >> O4 amber99_41 -0.55630 22 >> N3 amber99_35 -0.43400 23 >> H3 amber99_17 0.34200 24 >> C2 amber99_2 0.56770 25 >> O amber99_41 -0.58810 26 >> C3' amber99_11 0.07130 27 >> H3' amber99_19 0.09850 28 >> C2' amber99_11 -0.08540 29 >> H2'1 amber99_18 0.07180 30 >> H2'2 amber99_18 0.07180 31 >> O3' amber99_44 -0.52320 32 >> >> I can't see why atom 02 shouldn't be found. >> >> I am running GROMACS 4.0.5 on Mac OS 10.5 >> >> Thanks, >> Gunnar W. >> >> >> ------------------------------------------------------------------------ >> >> _______________________________________________ >> 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 >> > > -- > ======================================== > > 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-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 >
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