Hi justin, Ok i will explain more clearly what i really have is protein ligand complex from Autodock..I choose best complex based on predicted binding affinity. Using pymol i visualized complex.pdb and saved only ligand (ligand.pdb given below) and used swiss param tool online http://swissparam.ch/ to charmm 27 FF .itp file then i followed tutorial and ran 10ns simulation now wanted to use g_lie to calculate binding free energies..of this complex..so have to run one more simulation for ligand only in water right...for that im using coordinate file which i have saved it from pymol in original PDB file it is properly aligned :)
ATOM 1 C <1> d 83.432 21.209 56.133 -0.07 -0.02 C ATOM 2 C <1> d 84.828 21.291 56.786 -0.29 0.00 C ATOM 3 O <1> d 83.629 21.200 54.697 -0.02 -0.07 O ATOM 4 C <1> d 85.679 20.564 55.751 -0.19 -0.02 C ATOM 5 C <1> d 85.046 21.032 54.436 -0.15 0.04 C ATOM 6 N <1> d 82.546 22.305 56.532 -0.10 -0.05 N ATOM 7 C <1> d 81.884 22.186 57.757 0.18 0.05 C ATOM 8 N <1> d 81.028 23.185 58.155 0.01 -0.07 N ATOM 9 O <1> d 82.069 21.213 58.493 -0.09 0.04 O ATOM 10 C <1> d 80.868 24.232 57.405 -0.07 0.06 C ATOM 11 C <1> d 81.567 24.413 56.119 -0.49 0.00 C ATOM 12 C <1> d 82.377 23.424 55.745 -0.38 0.02 C ATOM 13 N <1> d 80.012 25.195 57.842 0.39 0.02 N ATOM 14 H <1> d 79.062 24.997 58.139 -0.05 -0.06 H ATOM 15 H <1> d 80.312 26.164 57.884 -0.11 -0.01 H ATOM 16 O <1> d 84.944 20.703 58.090 0.01 0.19 O ATOM 17 H <1> d 85.311 19.798 57.956 -0.17 -0.58 H ATOM 18 O <1> d 85.512 19.135 55.900 0.09 0.57 O ATOM 19 H <1> d 84.884 19.014 56.648 -0.30 -0.75 H ATOM 20 C <1> d 85.627 22.354 53.918 -0.22 0.11 C ATOM 21 O <1> d 84.597 23.194 53.394 -0.56 -0.44 O ATOM 22 H <1> d 83.757 22.697 53.521 0.27 0.18 H END Im running PDB2GMX to generate topol.top file..for this ligand by CHARMM 27 FF but it gives following error Fatal error: Residue '<1>' not found in residue topology database So now question how to solve this error..? Can you please suggest some help ? thanks, Nitin On Wed, Aug 8, 2012 at 12:08 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 8/8/12 5:37 AM, sai nitin wrote: >> >> Hi justin, >> >> Thanks for reply now i have ligand corrdinate file as follows >> >> ATOM 1 N A -13.006 -12.965 -0.251 -0.60 -0.09 N >> ATOM 2 C A -13.386 -13.020 1.035 -0.38 0.03 C >> ATOM 3 C A -13.037 -14.131 1.869 -0.32 -0.03 C >> ATOM 4 C A -12.284 -14.007 -0.761 -0.21 0.02 C >> ATOM 5 N A -11.897 -15.079 0.059 -0.24 -0.01 N >> ATOM 6 C A -12.288 -15.172 1.391 -0.37 0.01 C >> ATOM 7 N A -13.547 -13.886 3.036 -0.34 0.14 N >> ATOM 8 N A -14.076 -12.193 1.759 -0.27 0.01 N >> ATOM 9 C A -14.163 -12.729 2.956 -0.29 -0.08 C >> ATOM 10 N A -11.887 -13.919 -2.092 -0.05 0.04 N >> ATOM 11 H A -11.305 -15.802 -0.326 -0.11 -0.03 H >> ATOM 12 H A -12.027 -12.978 -2.454 -0.07 -0.16 H >> ATOM 13 C A -11.368 -14.845 -3.008 -0.39 0.00 C >> ATOM 14 C A -11.534 -14.731 -4.394 -0.49 0.00 C >> ATOM 15 C A -11.032 -15.710 -5.270 -0.32 0.00 C >> ATOM 16 C A -10.360 -16.822 -4.750 -0.24 0.00 C >> ATOM 17 C A -10.189 -16.950 -3.375 -0.33 0.00 C >> ATOM 18 C A -10.690 -15.970 -2.515 -0.42 0.00 C >> ATOM 19 C A -11.203 -15.559 -6.724 -0.27 0.00 C >> ATOM 20 C A -12.302 -15.958 -7.389 -0.19 0.02 C >> ATOM 21 O A -11.918 -16.240 2.152 -0.14 -0.09 O >> ATOM 22 H A -11.168 -16.702 1.710 -0.26 -0.13 H >> END >> >> Still not working >> >> Fatal error: >> Atom N in residue A 0 was not found in rtp entry RA with 32 atoms >> while sorting atoms. >> > > Your molecule has to correspond to some known entity in the force field. > Here, with the residue name "A," the closest match pdb2gmx can find is to > the ribonucleotide RA. If that's what this is, then your atom names need to > match with what is expected. > > It also appears your columns are still misaligned. > > -Justin > > >> Any help ?? >> >> Thanks, >> Nitin >> >> On Tue, Aug 7, 2012 at 11:42 AM, Justin Lemkul <jalem...@vt.edu> wrote: >>> >>> >>> >>> On 8/7/12 5:08 AM, sai nitin wrote: >>>> >>>> >>>> Hi all, >>>> >>>> Recently i performed protein ligand complex simulation my aim is to >>>> compute free energy values using g_lie..i came across that to perform >>>> g_lie analysis one should two 2 MD simulation one is protein ligand >>>> complex simulation (this is done ) used Charmm 27 FF second one is >>>> simulate ligand in water...which is the step i got stuck i know it is >>>> simple but couldnt get through first step it self preparing ligand >>>> coordinate file which i already have as follows i ran PDB2gmx to >>>> generate topol.top file but couldnt succeed.. ligand coordinate file >>>> is given below >>>> >>>> ATOM 1 N -13.006 -12.965 -0.251 1.00 0.00 N >>>> ATOM 2 C -13.386 -13.020 1.035 1.00 0.00 C >>>> ATOM 3 C1 -13.037 -14.131 1.869 1.00 0.00 C >>>> ATOM 4 C2 -12.284 -14.007 -0.761 1.00 0.00 C >>>> ATOM 5 N1 -11.897 -15.079 0.059 1.00 0.00 N >>>> ATOM 6 C3 -12.288 -15.172 1.391 1.00 0.00 C >>>> ATOM 7 N2 -13.547 -13.886 3.036 1.00 0.00 N >>>> ATOM 8 N3 -14.076 -12.193 1.759 1.00 0.00 N >>>> ATOM 9 C4 -14.163 -12.729 2.956 1.00 0.00 C >>>> ATOM 10 N4 -11.887 -13.919 -2.092 1.00 0.00 N >>>> ATOM 11 H -11.305 -15.802 -0.326 1.00 0.00 H >>>> ATOM 12 H1 -12.027 -12.978 -2.454 1.00 0.00 H >>>> ATOM 13 C5 -11.368 -14.845 -3.008 1.00 0.00 C >>>> ATOM 14 C6 -11.534 -14.731 -4.394 1.00 0.00 C >>>> ATOM 15 C7 -11.032 -15.710 -5.270 1.00 0.00 C >>>> ATOM 16 C8 -10.360 -16.822 -4.750 1.00 0.00 C >>>> ATOM 17 C9 -10.189 -16.950 -3.375 1.00 0.00 C >>>> ATOM 18 C10 -10.690 -15.970 -2.515 1.00 0.00 C >>>> ATOM 19 C11 -11.203 -15.559 -6.724 1.00 0.00 C >>>> ATOM 20 C12 -12.302 -15.958 -7.389 1.00 0.00 C >>>> ATOM 21 O -11.918 -16.240 2.152 1.00 0.00 O >>>> ATOM 22 H2 -11.168 -16.702 1.710 1.00 0.00 H >>>> ATOM 23 H3 -14.661 -12.289 3.746 1.00 0.00 H >>>> ATOM 24 H4 -12.034 -13.914 -4.779 1.00 0.00 H >>>> ATOM 25 H5 -9.992 -17.547 -5.386 1.00 0.00 H >>>> ATOM 26 H6 -9.692 -17.769 -2.991 1.00 0.00 H >>>> ATOM 27 H7 -10.559 -16.076 -1.497 1.00 0.00 H >>>> ATOM 28 H8 -10.438 -15.123 -7.263 1.00 0.00 H >>>> ATOM 29 H9 -13.084 -16.397 -6.878 1.00 0.00 H >>>> ATOM 30 H10 -12.364 -15.825 -8.411 1.00 0.00 H >>>> >>>> >>>> Running PDB2gmx gives error as follows >>>> >>>> Fatal error: >>>> Residue '-13.' not found in residue topology database >>>> >>>> >>>> Can any tell me what is wrong in my coordinate file .... >>>> >>> >>> It is formatted incorrectly. PDB format requires fixed spacing and >>> correct >>> content. The file shown above lacks a residue name column. >>> >>> -Justin >>> >>> -- >>> ======================================== >>> >>> Justin A. Lemkul, Ph.D. >>> Research Scientist >>> 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 >>> * Only plain text messages are allowed! >>> * Please search the archive at >>> http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists >> >> >> >> > > -- > ======================================== > > Justin A. Lemkul, Ph.D. > Research Scientist > 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 > * Only plain text messages are allowed! > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- Sainitin D PhD student Bioinformatics Group Biotechnology Center Technische Universität Dresden Tatzberg 47/49 01307 Dresden, Germany Tel Lab:+49 (0)351 463 40060 -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists