[gmx-users] Re: Error during executing the protein ligand tutorial
bharat gupta
bharat.85.monu at gmail.com
Tue Jun 21 06:51:05 CEST 2011
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 <jalemkul at 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>
>
> ==============================**==========
> --
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--
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 : monu46010 at yahoo.com
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