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:-<br>
<br><br>Fatal error:<br>Syntax error - File PTR.itp, line 7<br>Last line read:<br>'[ atomtypes ] '<br>Invalid order for directive atomtypes<br>For more information and tips for troubleshooting, please check the GROMACS<br>
website at <a href="http://www.gromacs.org/Documentation/Errors">http://www.gromacs.org/Documentation/Errors</a><br>-------------------------------------------------------<br><br>"Everything's formed from particles" (Van der Graaf Generator)<br>
<br>here's a list of output , I obtained till the step of adding ion ??<br><br><br><br><br><br>O/P - pdb2gmx command:-<br>+++++++++++++++++++++++++++<br><br>Checking for duplicate atoms....<br>Now there are 230 residues with 3606 atoms<br>
Making bonds...<br>Number of bonds was 3646, now 3646<br>Generating angles, dihedrals and pairs...<br>Before cleaning: 9583 pairs<br>Before cleaning: 9678 dihedrals<br>Keeping all generated dihedrals<br>Making cmap torsions...There are 228 cmap torsion pairs<br>
There are 9678 dihedrals, 618 impropers, 6593 angles<br> 9517 pairs, 3646 bonds and 0 virtual sites<br>Total mass 25776.218 a.m.u.<br>Total charge -2.000 e<br>Writing topology<br><br>Writing coordinate file...<br>
--------- PLEASE NOTE ------------<br>You have successfully generated a topology from: GFP_enzmod1.pdb.<br>The Charmm27 force field and the spce water model are used.<br> --------- ETON ESAELP ------------<br>
<br>gcq#139: "I Wrapped a Newspaper Round My Head" (F. Zappa)<br><br>================<br><br>changes made in conf.gro file :-<br>+++++++++++++++++++++++++++++++++<br><br> 230THR HG21 3601 -0.993 7.382 0.813<br>
230THR HG22 3602 -0.976 7.242 0.730<br> 230THR HG23 3603 -0.910 7.380 0.672<br> 230THR C 3604 -1.255 7.279 0.449<br> 230THR OT1 3605 -1.294 7.160 0.452<br> 230THR OT2 3606 -1.337 7.205 0.529<br>
1LIG C2 1 -0.905 -0.297 -0.859 <br> 1LIG C4 2 -0.546 1.023 -1.066 <br> 1LIG C5 3 0.009 -1.235 -0.411 <br> 1LIG C6 4 0.769 1.418 -0.818 <br> 1LIG C7 5 1.324 -0.840 -0.163 <br>
1LIG C8 6 1.704 0.487 -0.366 <br> 1LIG P 7 4.170 -0.099 0.400 <br> 1LIG O 8 -2.576 1.102 1.627 <br> 1LIG O1 9 2.986 0.872 -0.124 <br> 1LIG O2 10 -4.171 1.666 0.128 <br>
1LIG O3 11 4.434 -1.105 -0.839 <br> 1LIG O4 12 5.468 0.867 0.365 <br> 1LIG O5 13 3.920 -0.754 1.728 <br> 1LIG N 14 -4.640 -1.030 -0.361 <br> 1LIG C 15 -3.299 -0.614 0.075 <br>
1LIG C1 16 -2.331 -0.725 -1.128 <br> 1LIG C3 17 -3.413 0.823 0.594 <br> 1LIG H 18 -2.714 -0.120 -1.963 <br> 1LIG H3 19 -2.321 -1.757 -1.509 <br> 1LIG H4 20 -5.279 -1.040 0.434 <br>
1LIG H5 21 -4.610 -1.988 -0.710 <br> 1LIG H6 22 -1.265 1.756 -1.419 <br> 1LIG H7 23 -0.275 -2.271 -0.254 <br> 1LIG H8 24 1.059 2.453 -0.978 <br> 1LIG H9 25 2.016 -1.600 0.183 <br>
1LIG H10 26 -2.667 2.031 1.929 <br> 1LIG H11 27 5.079 -1.836 -0.728 <br> 1LIG H12 28 6.314 0.538 0.737 <br> 1LIG H1 29 -4.984 -0.408 -1.078 <br> 1LIG H2 30 -2.958 -1.266 0.879 <br>
5.23907 4.16174 3.66560<br><br>====================================<br><br>changes made in topol.top file:-<br>+++++++++++++++++++++++++++++++<br><br>;Include ligand topology<br>#include "PTR.itp"<br><br>
<br><br>[ molecules ]<br>; Compound #mols<br>Protein_chain_A 1<br>LIG 1<br><br>===============================<br> <br>O/P - editconf command:-<br>++++++++++++++++++++++++++++++<br><br>ead 3636 atoms<br>
Volume: 79.9234 nm^3, corresponds to roughly 35900 electrons<br>No velocities found<br> system size : 11.593 11.312 4.781 (nm)<br> diameter : 13.225 (nm)<br> center : 0.967 7.015 -1.015 (nm)<br>
box vectors : 5.239 4.162 3.666 (nm)<br> box angles : 90.00 90.00 90.00 (degrees)<br> box volume : 79.92 (nm^3)<br> shift : 6.645 0.598 8.627 (nm)<br>new center : 7.612 7.612 7.612 (nm)<br>
new box vectors : 15.225 15.225 15.225 (nm)<br>new box angles : 90.00 90.00 90.00 (degrees)<br>new box volume :3529.00 (nm^3)<br><br>gcq#188: "Clickety Clickety Click" (System Manager From Hell)<br>
<br>========================================<br><br><br>O/P - genbox command:-<br>++++++++++++++++++++++++<br><br>Reading solvent configuration<br>"216H2O,WATJP01,SPC216,SPC-MODEL,300K,BOX(M)=1.86206NM,WFVG,MAR. 1984"<br>
solvent configuration contains 648 atoms in 216 residues<br><br>Initialising van der waals distances...<br>Will generate new solvent configuration of 9x9x9 boxes<br>Generating configuration<br>Sorting configuration<br>Found 1 molecule type:<br>
SOL ( 3 atoms): 157464 residues<br>Calculating Overlap...<br>box_margin = 0.315<br>Removed 98544 atoms that were outside the box<br>Neighborsearching with a cut-off of 0.48<br>Table routines are used for coulomb: FALSE<br>
Table routines are used for vdw: FALSE<br>Cut-off's: NS: 0.48 Coulomb: 0.48 LJ: 0.48<br>System total charge: 0.000<br>Grid: 36 x 36 x 36 cells<br>Successfully made neighbourlist<br>nri = 567518, nrj = 17886927<br>
Checking Protein-Solvent overlap: tested 75752 pairs, removed 3738 atoms.<br>Checking Solvent-Solvent overlap: tested 1988826 pairs, removed 19455 atoms.<br>Added 116885 molecules<br>Generated solvent containing 350655 atoms in 116885 residues<br>
Writing generated configuration to solv.gro<br>Great Red Oystrich Makes All Chemists Sane<br><br>Output configuration contains 354291 atoms in 117116 residues<br>Volume : 3529 (nm^3)<br>Density : 1041.16 (g/l)<br>
Number of SOL molecules: 116885 <br><br>Processing topology<br>Adding line for 116885 solvent molecules to topology file (topol.top)<br><br>Back Off! I just backed up topol.top to ./#topol.top.1#<br><br>gcq#49: "You Could Make More Money As a Butcher" (F. Zappa)<br>
<br>===================================================================<br><br><br><br><br><br><br><br><br><div class="gmail_quote">On Tue, Jun 21, 2011 at 12:42 PM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;"><div class="im"><br>
<br>
bharat gupta wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Hi,<br>
<br>
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<br>
<br>
Fatal error:<br>
Group PTR not found in indexfile.<br>
"<br>
<br>
</blockquote>
<br></div>
I'm guessing you failed to follow step 5 here:<br>
<br>
<a href="http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field" target="_blank">http://www.gromacs.org/<u></u>Documentation/How-tos/Adding_<u></u>a_Residue_to_a_Force_Field</a><div class="im"><br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
also the charge on the system now is 8 .... pls help<br>
</blockquote>
<br></div>
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.<br>
<br>
-Justin<br>
<br>
-- <br>
==============================<u></u>==========<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | (540) 231-9080<br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.<u></u>vt.edu/Pages/Personal/justin</a><br>
<br>
==============================<u></u>==========<br><font color="#888888">
-- <br>
gmx-users mailing list <a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br>
<a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/<u></u>mailman/listinfo/gmx-users</a><br>
Please search the archive at <a href="http://www.gromacs.org/Support/Mailing_Lists/Search" target="_blank">http://www.gromacs.org/<u></u>Support/Mailing_Lists/Search</a> before posting!<br>
Please don't post (un)subscribe requests to the list. Use the www interface or send it to <a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a>.<br>
Can't post? Read <a href="http://www.gromacs.org/Support/Mailing_Lists" target="_blank">http://www.gromacs.org/<u></u>Support/Mailing_Lists</a><br>
</font></blockquote></div><br><br clear="all"><br>-- <br>Bharat<br>Ph.D. Candidate<br>Room No. : 7202A, 2nd Floor<br>Biomolecular Engineering Laboratory<br>Division of Chemical Engineering and Polymer Science<br>Pusan National University<br>
Busan -609735<br>South Korea<br>Lab phone no. - +82-51-510-3680, +82-51-583-8343<div>Mobile no. - 010-5818-3680<br>E-mail : <a href="mailto:monu46010@yahoo.com" target="_blank">monu46010@yahoo.com</a></div><br>