ok now I am doing the things again and here is the result of output of each command till adding ions. At the time of executing the command grompp for reading em.mdp file for ions.tpr generation, I am getting the following error:-
Fatal error: Syntax error - File PTR.itp, line 7 Last line read: '[ atomtypes ] ' Invalid order for directive atomtypes For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors ------------------------------------------------------- "Everything's formed from particles" (Van der Graaf Generator) here's a list of output , I obtained till the step of adding ion ?? O/P - pdb2gmx command:- +++++++++++++++++++++++++++ Checking for duplicate atoms.... Now there are 230 residues with 3606 atoms Making bonds... Number of bonds was 3646, now 3646 Generating angles, dihedrals and pairs... Before cleaning: 9583 pairs Before cleaning: 9678 dihedrals Keeping all generated dihedrals Making cmap torsions...There are 228 cmap torsion pairs There are 9678 dihedrals, 618 impropers, 6593 angles 9517 pairs, 3646 bonds and 0 virtual sites Total mass 25776.218 a.m.u. Total charge -2.000 e Writing topology Writing coordinate file... --------- PLEASE NOTE ------------ You have successfully generated a topology from: GFP_enzmod1.pdb. The Charmm27 force field and the spce water model are used. --------- ETON ESAELP ------------ gcq#139: "I Wrapped a Newspaper Round My Head" (F. Zappa) ================ changes made in conf.gro file :- +++++++++++++++++++++++++++++++++ 230THR HG21 3601 -0.993 7.382 0.813 230THR HG22 3602 -0.976 7.242 0.730 230THR HG23 3603 -0.910 7.380 0.672 230THR C 3604 -1.255 7.279 0.449 230THR OT1 3605 -1.294 7.160 0.452 230THR OT2 3606 -1.337 7.205 0.529 1LIG C2 1 -0.905 -0.297 -0.859 1LIG C4 2 -0.546 1.023 -1.066 1LIG C5 3 0.009 -1.235 -0.411 1LIG C6 4 0.769 1.418 -0.818 1LIG C7 5 1.324 -0.840 -0.163 1LIG C8 6 1.704 0.487 -0.366 1LIG P 7 4.170 -0.099 0.400 1LIG O 8 -2.576 1.102 1.627 1LIG O1 9 2.986 0.872 -0.124 1LIG O2 10 -4.171 1.666 0.128 1LIG O3 11 4.434 -1.105 -0.839 1LIG O4 12 5.468 0.867 0.365 1LIG O5 13 3.920 -0.754 1.728 1LIG N 14 -4.640 -1.030 -0.361 1LIG C 15 -3.299 -0.614 0.075 1LIG C1 16 -2.331 -0.725 -1.128 1LIG C3 17 -3.413 0.823 0.594 1LIG H 18 -2.714 -0.120 -1.963 1LIG H3 19 -2.321 -1.757 -1.509 1LIG H4 20 -5.279 -1.040 0.434 1LIG H5 21 -4.610 -1.988 -0.710 1LIG H6 22 -1.265 1.756 -1.419 1LIG H7 23 -0.275 -2.271 -0.254 1LIG H8 24 1.059 2.453 -0.978 1LIG H9 25 2.016 -1.600 0.183 1LIG H10 26 -2.667 2.031 1.929 1LIG H11 27 5.079 -1.836 -0.728 1LIG H12 28 6.314 0.538 0.737 1LIG H1 29 -4.984 -0.408 -1.078 1LIG H2 30 -2.958 -1.266 0.879 5.23907 4.16174 3.66560 ==================================== changes made in topol.top file:- +++++++++++++++++++++++++++++++ ;Include ligand topology #include "PTR.itp" [ molecules ] ; Compound #mols Protein_chain_A 1 LIG 1 =============================== O/P - editconf command:- ++++++++++++++++++++++++++++++ ead 3636 atoms Volume: 79.9234 nm^3, corresponds to roughly 35900 electrons No velocities found system size : 11.593 11.312 4.781 (nm) diameter : 13.225 (nm) center : 0.967 7.015 -1.015 (nm) box vectors : 5.239 4.162 3.666 (nm) box angles : 90.00 90.00 90.00 (degrees) box volume : 79.92 (nm^3) shift : 6.645 0.598 8.627 (nm) new center : 7.612 7.612 7.612 (nm) new box vectors : 15.225 15.225 15.225 (nm) new box angles : 90.00 90.00 90.00 (degrees) new box volume :3529.00 (nm^3) gcq#188: "Clickety Clickety Click" (System Manager From Hell) ======================================== O/P - genbox command:- ++++++++++++++++++++++++ Reading solvent configuration "216H2O,WATJP01,SPC216,SPC-MODEL,300K,BOX(M)=1.86206NM,WFVG,MAR. 1984" solvent configuration contains 648 atoms in 216 residues Initialising van der waals distances... Will generate new solvent configuration of 9x9x9 boxes Generating configuration Sorting configuration Found 1 molecule type: SOL ( 3 atoms): 157464 residues Calculating Overlap... box_margin = 0.315 Removed 98544 atoms that were outside the box Neighborsearching with a cut-off of 0.48 Table routines are used for coulomb: FALSE Table routines are used for vdw: FALSE Cut-off's: NS: 0.48 Coulomb: 0.48 LJ: 0.48 System total charge: 0.000 Grid: 36 x 36 x 36 cells Successfully made neighbourlist nri = 567518, nrj = 17886927 Checking Protein-Solvent overlap: tested 75752 pairs, removed 3738 atoms. Checking Solvent-Solvent overlap: tested 1988826 pairs, removed 19455 atoms. Added 116885 molecules Generated solvent containing 350655 atoms in 116885 residues Writing generated configuration to solv.gro Great Red Oystrich Makes All Chemists Sane Output configuration contains 354291 atoms in 117116 residues Volume : 3529 (nm^3) Density : 1041.16 (g/l) Number of SOL molecules: 116885 Processing topology Adding line for 116885 solvent molecules to topology file (topol.top) Back Off! I just backed up topol.top to ./#topol.top.1# gcq#49: "You Could Make More Money As a Butcher" (F. Zappa) =================================================================== On Tue, Jun 21, 2011 at 12:42 PM, Justin A. Lemkul <jalem...@vt.edu> wrote: > > > bharat gupta wrote: > >> Hi, >> >> In addition to my last mail, I am also getting another error during the >> minimization step. I made the changes in em_real.mdp file for my sytem but >> its showing the error that "ource code file: readir.c, line: 1316 >> >> Fatal error: >> Group PTR not found in indexfile. >> " >> >> > I'm guessing you failed to follow step 5 here: > > http://www.gromacs.org/**Documentation/How-tos/Adding_** > a_Residue_to_a_Force_Field<http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field> > > > also the charge on the system now is 8 .... pls help >> > > Take another look at the screen output regarding net charge before adding > ions. I suspect you're missing an exponent. But I'd echo what Mark has > said - always provide real output directly copied from the screen, or else > we're left to our suspicions and guesses, which ends up wasting everyone's > time. > > -Justin > > -- > ==============================**========== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<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<http://lists.gromacs.org/mailman/listinfo/gmx-users> > Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<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<http://www.gromacs.org/Support/Mailing_Lists> > -- Bharat Ph.D. Candidate Room No. : 7202A, 2nd Floor Biomolecular Engineering Laboratory Division of Chemical Engineering and Polymer Science Pusan National University Busan -609735 South Korea Lab phone no. - +82-51-510-3680, +82-51-583-8343 Mobile no. - 010-5818-3680 E-mail : monu46...@yahoo.com
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