[gmx-users] Grompp failed under double precision
Jack Shultz
js at drugdiscoveryathome.com
Mon Dec 7 01:07:07 CET 2009
We have a workflow going, and I switched to double precision because
of the LINCS issues. I got this error now with grompp. I don't think
anything else is different other than double precision, but I included
the logs for this.
-------------------------------------------------------
Program grompp_d, VERSION 4.0.5
Source code file: toppush.c, line: 1273
Fatal error:
[ file spce.itp, line 32 ]:
Atom index (1) in bonds out of bounds (1-0).
This probably means that you have inserted topology section "bonds"
in a part belonging to a different molecule than you intended to.
In that case move the "bonds" section to the right molecule.
-------------------------------------------------------
--
Jack
http://drugdiscoveryathome.com
http://hydrogenathome.org
-------------- next part --------------
Name "main::make_ndx" used only once: possible typo at bin/mdrun.pl line 45.
Name "main::rsc_memory_bound" used only once: possible typo at bin/mdrun.pl line 23.
Name "main::g_energy" used only once: possible typo at bin/mdrun.pl line 47.
Name "main::protein_lig" used only once: possible typo at bin/mdrun.pl line 46.
Name "main::TOP_SCORE" used only once: possible typo at bin/mdrun.pl line 482.
4
Checking if script is running
php clear_assignments.php
mkdir /home/boincadm/projects/DrugDiscovery/sample_results/tmp
mv /home/boincadm/projects/DrugDiscovery/sample_results/autodock_*.7z /home/boincadm/projects/DrugDiscovery/sample_results/tmp
4
Checking if script is running
/home/boincadm/projects/DrugDiscovery/sample_results/tmp/autodock_ga_run_10_bt_fzd8min_renum_SS.pdb_lig_omega_000070_ts_1260032146055243000.7z
rm -rf /home/boincadm/projects/DrugDiscovery/sample_results/tmp/autodock_ga_run_10_bt_fzd8min_renum_SS.pdb_lig_omega_000070_ts_1260032146055243000
mkdir /home/boincadm/projects/DrugDiscovery/sample_results/tmp/autodock_ga_run_10_bt_fzd8min_renum_SS.pdb_lig_omega_000070_ts_1260032146055243000
cp /home/boincadm/projects/DrugDiscovery/bin/receptor.pdb /home/boincadm/projects/DrugDiscovery/sample_results/tmp/autodock_ga_run_10_bt_fzd8min_renum_SS.pdb_lig_omega_000070_ts_1260032146055243000
7za e -y -o/home/boincadm/projects/DrugDiscovery/sample_results/tmp/autodock_ga_run_10_bt_fzd8min_renum_SS.pdb_lig_omega_000070_ts_1260032146055243000 /home/boincadm/projects/DrugDiscovery/sample_results/tmp/autodock_ga_run_10_bt_fzd8min_renum_SS.pdb_lig_omega_000070_ts_1260032146055243000.7z
7-Zip (A) 4.61 beta Copyright (c) 1999-2008 Igor Pavlov 2008-11-23
p7zip Version 4.61 (locale=en_US.UTF-8,Utf16=on,HugeFiles=on,2 CPUs)
Processing archive: /home/boincadm/projects/DrugDiscovery/sample_results/tmp/autodock_ga_run_10_bt_fzd8min_renum_SS.pdb_lig_omega_000070_ts_1260032146055243000.7z
Extracting out.dlg
Extracting job.xml
Extracting ligand_receptor.dpf
Extracting out.glg
Extracting receptor.gpf
Everything is Ok
Files: 5
Size: 553641
Compressed: 56651
/usr/local/bin/pythonsh /usr/local/MGLTools-1.5.4/MGLToolsPckgs/AutoDockTools/Utilities24/summarize_results4.py -v -d /home/boincadm/projects/DrugDiscovery/sample_results/tmp/autodock_ga_run_10_bt_fzd8min_renum_SS.pdb_lig_omega_000070_ts_1260032146055243000 -r receptor.pdb -o /home/boincadm/projects/DrugDiscovery/sample_results/tmp/autodock_ga_run_10_bt_fzd8min_renum_SS.pdb_lig_omega_000070_ts_1260032146055243000_summary.txt
setting PYTHONHOME environment
set verbose to True
set directory to /home/boincadm/projects/DrugDiscovery/sample_results/tmp/autodock_ga_run_10_bt_fzd8min_renum_SS.pdb_lig_omega_000070_ts_1260032146055243000
set receptor_filename to receptor.pdb
set outputfilename to /home/boincadm/projects/DrugDiscovery/sample_results/tmp/autodock_ga_run_10_bt_fzd8min_renum_SS.pdb_lig_omega_000070_ts_1260032146055243000_summary.txt
first is True
rm -rf /home/boincadm/projects/DrugDiscovery/sample_results/tmp/autodock_ga_run_10_bt_fzd8min_renum_SS.pdb_lig_omega_000070_ts_1260032146055243000
5
Checking if script is running
/home/boincadm/projects/DrugDiscovery/sample_results/tmp/autodock_ga_run_10_bt_fzd8min_renum_SS.pdb_lig_omega_000248_ts_1260044614686460000.7z
rm -rf /home/boincadm/projects/DrugDiscovery/sample_results/tmp/autodock_ga_run_10_bt_fzd8min_renum_SS.pdb_lig_omega_000248_ts_1260044614686460000
mkdir /home/boincadm/projects/DrugDiscovery/sample_results/tmp/autodock_ga_run_10_bt_fzd8min_renum_SS.pdb_lig_omega_000248_ts_1260044614686460000
cp /home/boincadm/projects/DrugDiscovery/bin/receptor.pdb /home/boincadm/projects/DrugDiscovery/sample_results/tmp/autodock_ga_run_10_bt_fzd8min_renum_SS.pdb_lig_omega_000248_ts_1260044614686460000
7za e -y -o/home/boincadm/projects/DrugDiscovery/sample_results/tmp/autodock_ga_run_10_bt_fzd8min_renum_SS.pdb_lig_omega_000248_ts_1260044614686460000 /home/boincadm/projects/DrugDiscovery/sample_results/tmp/autodock_ga_run_10_bt_fzd8min_renum_SS.pdb_lig_omega_000248_ts_1260044614686460000.7z
7-Zip (A) 4.61 beta Copyright (c) 1999-2008 Igor Pavlov 2008-11-23
p7zip Version 4.61 (locale=en_US.UTF-8,Utf16=on,HugeFiles=on,2 CPUs)
Processing archive: /home/boincadm/projects/DrugDiscovery/sample_results/tmp/autodock_ga_run_10_bt_fzd8min_renum_SS.pdb_lig_omega_000248_ts_1260044614686460000.7z
Extracting out.dlg
Extracting job.xml
Extracting ligand_receptor.dpf
Extracting out.glg
Extracting receptor.gpf
Everything is Ok
Files: 5
Size: 532380
Compressed: 54948
/usr/local/bin/pythonsh /usr/local/MGLTools-1.5.4/MGLToolsPckgs/AutoDockTools/Utilities24/summarize_results4.py -v -d /home/boincadm/projects/DrugDiscovery/sample_results/tmp/autodock_ga_run_10_bt_fzd8min_renum_SS.pdb_lig_omega_000248_ts_1260044614686460000 -r receptor.pdb -o /home/boincadm/projects/DrugDiscovery/sample_results/tmp/autodock_ga_run_10_bt_fzd8min_renum_SS.pdb_lig_omega_000248_ts_1260044614686460000_summary.txt
setting PYTHONHOME environment
set verbose to True
set directory to /home/boincadm/projects/DrugDiscovery/sample_results/tmp/autodock_ga_run_10_bt_fzd8min_renum_SS.pdb_lig_omega_000248_ts_1260044614686460000
set receptor_filename to receptor.pdb
set outputfilename to /home/boincadm/projects/DrugDiscovery/sample_results/tmp/autodock_ga_run_10_bt_fzd8min_renum_SS.pdb_lig_omega_000248_ts_1260044614686460000_summary.txt
first is True
rm -rf /home/boincadm/projects/DrugDiscovery/sample_results/tmp/autodock_ga_run_10_bt_fzd8min_renum_SS.pdb_lig_omega_000248_ts_1260044614686460000
4
Checking if script is running
/home/boincadm/projects/DrugDiscovery/sample_results/tmp/autodock_ga_run_10_bt_fzd8min_renum_SS.pdb_lig_omega_000340_ts_1260050818200871000.7z
rm -rf /home/boincadm/projects/DrugDiscovery/sample_results/tmp/autodock_ga_run_10_bt_fzd8min_renum_SS.pdb_lig_omega_000340_ts_1260050818200871000
mkdir /home/boincadm/projects/DrugDiscovery/sample_results/tmp/autodock_ga_run_10_bt_fzd8min_renum_SS.pdb_lig_omega_000340_ts_1260050818200871000
cp /home/boincadm/projects/DrugDiscovery/bin/receptor.pdb /home/boincadm/projects/DrugDiscovery/sample_results/tmp/autodock_ga_run_10_bt_fzd8min_renum_SS.pdb_lig_omega_000340_ts_1260050818200871000
7za e -y -o/home/boincadm/projects/DrugDiscovery/sample_results/tmp/autodock_ga_run_10_bt_fzd8min_renum_SS.pdb_lig_omega_000340_ts_1260050818200871000 /home/boincadm/projects/DrugDiscovery/sample_results/tmp/autodock_ga_run_10_bt_fzd8min_renum_SS.pdb_lig_omega_000340_ts_1260050818200871000.7z
7-Zip (A) 4.61 beta Copyright (c) 1999-2008 Igor Pavlov 2008-11-23
p7zip Version 4.61 (locale=en_US.UTF-8,Utf16=on,HugeFiles=on,2 CPUs)
Processing archive: /home/boincadm/projects/DrugDiscovery/sample_results/tmp/autodock_ga_run_10_bt_fzd8min_renum_SS.pdb_lig_omega_000340_ts_1260050818200871000.7z
Extracting out.dlg
Extracting job.xml
Extracting ligand_receptor.dpf
Extracting out.glg
Extracting receptor.gpf
Everything is Ok
Files: 5
Size: 515347
Compressed: 54218
/usr/local/bin/pythonsh /usr/local/MGLTools-1.5.4/MGLToolsPckgs/AutoDockTools/Utilities24/summarize_results4.py -v -d /home/boincadm/projects/DrugDiscovery/sample_results/tmp/autodock_ga_run_10_bt_fzd8min_renum_SS.pdb_lig_omega_000340_ts_1260050818200871000 -r receptor.pdb -o /home/boincadm/projects/DrugDiscovery/sample_results/tmp/autodock_ga_run_10_bt_fzd8min_renum_SS.pdb_lig_omega_000340_ts_1260050818200871000_summary.txt
setting PYTHONHOME environment
set verbose to True
set directory to /home/boincadm/projects/DrugDiscovery/sample_results/tmp/autodock_ga_run_10_bt_fzd8min_renum_SS.pdb_lig_omega_000340_ts_1260050818200871000
set receptor_filename to receptor.pdb
set outputfilename to /home/boincadm/projects/DrugDiscovery/sample_results/tmp/autodock_ga_run_10_bt_fzd8min_renum_SS.pdb_lig_omega_000340_ts_1260050818200871000_summary.txt
first is True
rm -rf /home/boincadm/projects/DrugDiscovery/sample_results/tmp/autodock_ga_run_10_bt_fzd8min_renum_SS.pdb_lig_omega_000340_ts_1260050818200871000
cat /home/boincadm/projects/DrugDiscovery/sample_results/tmp/*_summary.txt > /home/boincadm/projects/DrugDiscovery/sample_results/tmp/summary_1.0.txt
sed '/#dlgfn #in cluster #LE #rmsd #ats #tors/d' /home/boincadm/projects/DrugDiscovery/sample_results/tmp/summary_1.0.txt > /home/boincadm/projects/DrugDiscovery/sample_results/tmp/summary_2.0.txt
cat /home/boincadm/projects/DrugDiscovery/sample_results/tmp/summary_2.0.txt | sort -k3n -t, > /home/boincadm/projects/DrugDiscovery/sample_results/tmp/summary_2.0.sort
rm -rf /home/boincadm/projects/DrugDiscovery/sample_results/tmp/*.txt
cat /home/boincadm/projects/DrugDiscovery/sample_results/tmp/summary_2.0.sort | awk '{ print substr( $0, 0, match($0, /,/) - 5 ) }' | sed -n 'G; s/\n/&&/; /^\([ -~]*\n\).*\n\1/d; s/\n//; h; P' > /home/boincadm/projects/DrugDiscovery/sample_results/tmp/summary_3.0.sort && echo EOF >> /home/boincadm/projects/DrugDiscovery/sample_results/tmp/summary_3.0.sort
cat /home/boincadm/projects/DrugDiscovery/sample_results/tmp/summary_3.0.sort | sed '$!N; /^\(.*\)\n\1$/!P; D' > /home/boincadm/projects/DrugDiscovery/sample_results/tmp/tmp.txt && cp /home/boincadm/projects/DrugDiscovery/sample_results/tmp/tmp.txt /home/boincadm/projects/DrugDiscovery/sample_results/tmp/summary_3.0.sort
59% full
/home/boincadm/projects/DrugDiscovery/sample_results/tmp/autodock_ga_run_10_bt_fzd8min_renum_SS.pdb_lig_omega_000340_ts_1260050818200871000
mkdir /home/boincadm/projects/DrugDiscovery/sample_results/tmp/autodock_ga_run_10_bt_fzd8min_renum_SS.pdb_lig_omega_000340_ts_1260050818200871000
7za e -o/home/boincadm/projects/DrugDiscovery/sample_results/tmp/autodock_ga_run_10_bt_fzd8min_renum_SS.pdb_lig_omega_000340_ts_1260050818200871000 /home/boincadm/projects/DrugDiscovery/sample_results/tmp/autodock_ga_run_10_bt_fzd8min_renum_SS.pdb_lig_omega_000340_ts_1260050818200871000.7z
7-Zip (A) 4.61 beta Copyright (c) 1999-2008 Igor Pavlov 2008-11-23
p7zip Version 4.61 (locale=en_US.UTF-8,Utf16=on,HugeFiles=on,2 CPUs)
Processing archive: /home/boincadm/projects/DrugDiscovery/sample_results/tmp/autodock_ga_run_10_bt_fzd8min_renum_SS.pdb_lig_omega_000340_ts_1260050818200871000.7z
Extracting out.dlg
Extracting job.xml
Extracting ligand_receptor.dpf
Extracting out.glg
Extracting receptor.gpf
Everything is Ok
Files: 5
Size: 515347
Compressed: 54218
/home/boincadm/projects/DrugDiscovery/sample_results/tmp/autodock_ga_run_10_bt_fzd8min_renum_SS.pdb_lig_omega_000340_ts_1260050818200871000
bt: fzd8min_renum_SS.pdb
lig: omega_000340
ts: 1260050818200871000
nsteps_5000_int_0_-_500_bt_fzd8min_renum_SS.pdb_lig_omega_000340_ts_1260143758535223000
/usr/local/bin/pythonsh /usr/local/MGLTools-1.5.4/MGLToolsPckgs/AutoDockTools/Utilities24/write_largest_cluster_ligand.py
setting PYTHONHOME environment
/home/boincadm/projects/DrugDiscovery/sample_results/tmp/autodock_ga_run_10_bt_fzd8min_renum_SS.pdb_lig_omega_000340_ts_1260050818200871000/ligand_BC.pdbqt
Filesize: 2625
/usr/local/bin/pythonsh /usr/local/MGLTools-1.5.4/MGLToolsPckgs/AutoDockTools/Utilities24/pdbqt_to_pdb.py -f ligand_BC.pdbqt -o ligand_BC.pdb
setting PYTHONHOME environment
1 molecule converted
25 audit log messages
babel -ipdb ligand_BC.pdb -opdb ligand_BC.pdb -h
sed -i 's/UNL/LIG/g' ligand_BC.pdb
grep LIG ligand_BC.pdb > Ligand.pdb
/usr/local/bin/acpypi -n 0 -i Ligand.pdb -s 240
====================================================================================================
| ACPYPI: AnteChamber PYthon Parser Interface v. 2009-07-19 21:42:04Z Rev: 251 (c) 2008-2009 AWSdS |
====================================================================================================
==> ... charge set to 0
==> ... converting pdb input file to mol2 input file
==> * Babel OK *
==> Executing Antechamber...
==> * Antechamber OK *
==> * Parmchk OK *
==> Executing Tleap...
++++++++++start_quote+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Checking 'LIG'....
Warning: Close contact of 1.996421 angstroms between .R<LIG 1>.A<H5 31> and .R<LIG 1>.A<H15 41>
Checking parameters for unit 'LIG'.
Checking for bond parameters.
Checking for angle parameters.
check: Warnings: 1
Unit is OK.
++++++++++end_quote+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
==> * Tleap OK *
==> Removing temporary files...
==> Writing NEW PDB file
==> Writing CNS/XPLOR files
==> Writing GROMACS files
==> Writing CHARMM files
==> Writing pickle file Ligand.pkl
Total time of execution: 11s
cp /home/boincadm/projects/DrugDiscovery/bin/ProteinAmber.pdb .
pdb2gmx_d -ff amber99sb -f ProteinAmber.pdb -o Protein2.pdb -p Protein.top -water spce -ignh
:-) G R O M A C S (-:
Gyas ROwers Mature At Cryogenic Speed
:-) VERSION 4.0.5 (-:
Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2008, The GROMACS development team,
check out http://www.gromacs.org for more information.
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License
as published by the Free Software Foundation; either version 2
of the License, or (at your option) any later version.
:-) pdb2gmx_d (double precision) (-:
Option Filename Type Description
------------------------------------------------------------
-f ProteinAmber.pdb Input Structure file: gro g96 pdb tpr tpb tpa
-o Protein2.pdb Output Structure file: gro g96 pdb
-p Protein.top Output Topology file
-i posre.itp Output Include file for topology
-n clean.ndx Output, Opt. Index file
-q clean.pdb Output, Opt. Structure file: gro g96 pdb
Option Type Value Description
------------------------------------------------------
-[no]h bool no Print help info and quit
-nice int 0 Set the nicelevel
-[no]merge bool no Merge chains into one molecule definition
-ff string amber99sb Force field, interactive by default. Use -h
for information.
-water enum spce Water model to use: with GROMOS we recommend SPC,
with OPLS, TIP4P: spc, spce, tip3p, tip4p, tip5p
or f3c
-[no]inter bool no Set the next 8 options to interactive
-[no]ss bool no Interactive SS bridge selection
-[no]ter bool no Interactive termini selection, iso charged
-[no]lys bool no Interactive Lysine selection, iso charged
-[no]arg bool no Interactive Arganine selection, iso charged
-[no]asp bool no Interactive Aspartic Acid selection, iso charged
-[no]glu bool no Interactive Glutamic Acid selection, iso charged
-[no]gln bool no Interactive Glutamine selection, iso neutral
-[no]his bool no Interactive Histidine selection, iso checking
H-bonds
-angle real 135 Minimum hydrogen-donor-acceptor angle for a
H-bond (degrees)
-dist real 0.3 Maximum donor-acceptor distance for a H-bond (nm)
-[no]una bool no Select aromatic rings with united CH atoms on
Phenylalanine, Tryptophane and Tyrosine
-[no]ignh bool yes Ignore hydrogen atoms that are in the pdb file
-[no]missing bool no Continue when atoms are missing, dangerous
-[no]v bool no Be slightly more verbose in messages
-posrefc real 1000 Force constant for position restraints
-vsite enum none Convert atoms to virtual sites: none, hydrogens
or aromatics
-[no]heavyh bool no Make hydrogen atoms heavy
-[no]deuterate bool no Change the mass of hydrogens to 2 amu
Opening library file /usr/local/gromacs/share/gromacs/top/ffamber99sb.rtp
Opening library file /usr/local/gromacs/share/gromacs/top/aminoacids.dat
Opening library file /usr/local/gromacs/share/gromacs/top/aminoacids.dat
Opening library file /usr/local/gromacs/share/gromacs/top/atommass.dat
Opening library file /usr/local/gromacs/share/gromacs/top/vdwradii.dat
Opening library file /usr/local/gromacs/share/gromacs/top/dgsolv.dat
Opening library file /usr/local/gromacs/share/gromacs/top/electroneg.dat
Opening library file /usr/local/gromacs/share/gromacs/top/elements.dat
Opening library file /usr/local/gromacs/share/gromacs/top/xlateat.dat
26 out of 26 lines of xlateat.dat converted succesfully
All occupancies are one
Opening library file /usr/local/gromacs/share/gromacs/top/ffamber99sb.atp
Atomtype 1
Atomtype 1
Atomtype 1
Atomtype 1
Atomtype 1
Atomtype 1
Atomtype 1
Atomtype 1
Atomtype 1
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Atomtype 1
Atomtype 1
Atomtype 1
Atomtype 1
Atomtype 1
Atomtype 1
Atomtype 1
Atomtype 1
Atomtype 1
Atomtype 1
Atomtype 1
Atomtype 1
Atomtype 1
Atomtype 1
Atomtype 1
Atomtype 1
Atomtype 1
Atomtype 1
Atomtype 1
Atomtype 1
Atomtype 1
Atomtype 1
Atomtype 1
Atomtype 1
Atomtype 1
Opening library file /usr/local/gromacs/share/gromacs/top/ffamber99sb.rtp
Residue 1
Residue 2
Residue 3
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Sorting it all out...
Opening library file /usr/local/gromacs/share/gromacs/top/ffamber99sb.hdb
Opening library file /usr/local/gromacs/share/gromacs/top/ffamber99sb-n.tdb
Opening library file /usr/local/gromacs/share/gromacs/top/ffamber99sb-c.tdb
There are 362 donors and 360 acceptors
There are 560 hydrogen bonds
Opening library file /usr/local/gromacs/share/gromacs/top/specbond.dat
7 out of 7 lines of specbond.dat converted succesfully
Special Atom Distance matrix:
MET22 MET60 MET91 MET102 MET118 MET144 MET182
SD170 SD483 SD720 SD820 SD945 SD1158 SD1471
MET60 SD483 1.393
MET91 SD720 2.283 1.311
MET102 SD820 1.709 0.708 0.645
MET118 SD945 1.580 1.005 1.973 1.522
MET144 SD1158 4.060 3.768 4.835 4.406 3.005
MET182 SD1471 3.767 3.144 3.961 3.663 2.350 1.316
MET213 SD1708 5.099 4.251 4.840 4.672 3.594 2.229 1.451
MET224 SD1808 4.355 3.647 4.395 4.140 2.913 1.480 0.619
MET240 SD1933 2.788 2.012 2.992 2.600 1.472 1.930 1.306
MET213 MET224
SD1708 SD1808
MET224 SD1808 0.866
MET240 SD1933 2.427 1.747
Making bonds...
Opening library file /usr/local/gromacs/share/gromacs/top/aminoacids.dat
Number of bonds was 3924, now 3922
Generating angles, dihedrals and pairs...
Before cleaning: 10294 pairs
Before cleaning: 10454 dihedrals
Keeping all generated dihedrals
There are 10454 dihedrals, 810 impropers, 7078 angles
10210 pairs, 3922 bonds and 0 virtual sites
Total mass 28352.724 a.m.u.
Total charge -8.000 e
Writing topology
Writing coordinate file...
WARNING: masses will be determined based on residue and atom names,
this can deviate from the real mass of the atom type
Entries in atommass.dat: 178
WARNING: vdwradii will be determined based on residue and atom names,
this can deviate from the real mass of the atom type
Entries in vdwradii.dat: 29
Entries in dgsolv.dat: 7
Entries in electroneg.dat: 71
Entries in elements.dat: 218
Reading ProteinAmber.pdb...
Read 1976 atoms
Analyzing pdb file
There are 1 chains and 0 blocks of water and 244 residues with 1976 atoms
chain #res #atoms
1 ' ' 244 1976
Reading residue database... (ffamber99sb)
Processing chain 1 (1976 atoms, 244 residues)
Checking for duplicate atoms....
N-terminus: none
C-terminus: none
Now there are 244 residues with 3864 atoms
--------- PLEASE NOTE ------------
You have succesfully generated a topology from: ProteinAmber.pdb.
The amber99sb force field and the spce water model are used.
Note that the default mechanism for selecting a force fields has
changed, starting from GROMACS version 3.2.0
--------- ETON ESAELP ------------
gcq#152: "I Smell Smoke From a Gun Named Extinction" (Pixies)
grep -h ATOM Protein2.pdb Ligand.acpypi/Ligand_NEW.pdb >| Complex.pdb
cp Ligand.acpypi/Ligand_GMX.itp Ligand.itp
cp Protein.top Complex.top
cat Complex.top | sed '/#include \"ffamber99sb.itp\"/a #include "Ligand.itp"' >| Complex2.top
echo "Ligand 1" >> Complex2.top
mv Complex2.top Complex.top
cp /home/boincadm/projects/DrugDiscovery/bin/em.mdp .
editconf_d -bt triclinic -f Complex.pdb -o Complex.pdb -d 1.0
:-) G R O M A C S (-:
Gnomes, ROck Monsters And Chili Sauce
:-) VERSION 4.0.5 (-:
Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2008, The GROMACS development team,
check out http://www.gromacs.org for more information.
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License
as published by the Free Software Foundation; either version 2
of the License, or (at your option) any later version.
:-) editconf_d (double precision) (-:
Option Filename Type Description
------------------------------------------------------------
-f Complex.pdb Input Structure file: gro g96 pdb tpr tpb tpa
-n index.ndx Input, Opt. Index file
-o Complex.pdb Output, Opt! Structure file: gro g96 pdb
-mead mead.pqr Output, Opt. Coordinate file for MEAD
-bf bfact.dat Input, Opt. Generic data file
Option Type Value Description
------------------------------------------------------
-[no]h bool no Print help info and quit
-nice int 0 Set the nicelevel
-[no]w bool no View output xvg, xpm, eps and pdb files
-[no]ndef bool no Choose output from default index groups
-bt enum triclinic Box type for -box and -d: triclinic, cubic,
dodecahedron or octahedron
-box vector 0 0 0 Box vector lengths (a,b,c)
-angles vector 90 90 90 Angles between the box vectors (bc,ac,ab)
-d real 1 Distance between the solute and the box
-[no]c bool no Center molecule in box (implied by -box and -d)
-center vector 0 0 0 Coordinates of geometrical center
-translate vector 0 0 0 Translation
-rotate vector 0 0 0 Rotation around the X, Y and Z axes in degrees
-[no]princ bool no Orient molecule(s) along their principal axes
-scale vector 1 1 1 Scaling factor
-density real 1000 Density (g/l) of the output box achieved by
scaling
-[no]pbc bool no Remove the periodicity (make molecule whole again)
-[no]grasp bool no Store the charge of the atom in the B-factor
field and the radius of the atom in the occupancy
field
-rvdw real 0.12 Default Van der Waals radius (in nm) if one can
not be found in the database or if no parameters
are present in the topology file
-sig56 real 0 Use rmin/2 (minimum in the Van der Waals
potential) rather than sigma/2
-[no]vdwread bool no Read the Van der Waals radii from the file
vdwradii.dat rather than computing the radii
based on the force field
-[no]atom bool no Force B-factor attachment per atom
-[no]legend bool no Make B-factor legend
-label string A Add chain label for all residues
Opening library file /usr/local/gromacs/share/gromacs/top/aminoacids.dat
Opening library file /usr/local/gromacs/share/gromacs/top/atommass.dat
Opening library file /usr/local/gromacs/share/gromacs/top/vdwradii.dat
Opening library file /usr/local/gromacs/share/gromacs/top/dgsolv.dat
Opening library file /usr/local/gromacs/share/gromacs/top/electroneg.dat
Opening library file /usr/local/gromacs/share/gromacs/top/elements.dat
Back Off! I just backed up Complex.pdb to ./#Complex.pdb.1#
gcq#152: "I Smell Smoke From a Gun Named Extinction" (Pixies)
WARNING: masses will be determined based on residue and atom names,
this can deviate from the real mass of the atom type
Entries in atommass.dat: 178
WARNING: vdwradii will be determined based on residue and atom names,
this can deviate from the real mass of the atom type
Entries in vdwradii.dat: 29
Entries in dgsolv.dat: 7
Entries in electroneg.dat: 71
Entries in elements.dat: 218
Read 3911 atoms
No velocities found
system size : 6.660 4.981 4.130 (nm)
center : -0.836 -0.939 0.497 (nm)
box vectors : 0.000 0.000 0.000 (nm)
box angles : 0.00 0.00 0.00 (degrees)
box volume : 0.00 (nm^3)
shift : 5.166 4.429 2.568 (nm)
new center : 4.330 3.491 3.065 (nm)
new box vectors : 8.660 6.981 6.130 (nm)
new box angles : 90.00 90.00 90.00 (degrees)
new box volume : 370.58 (nm^3)
WARNING: No boxtype specified - distance condition applied in each dimension.
If the molecule rotates the actual distance will be smaller. You might want
to use a cubic box instead, or why not try a dodecahedron today?
genbox_d -cp Complex.pdb -cs ffamber_tip3p.gro -o Complex_b4ion.pdb -p Complex.top
:-) G R O M A C S (-:
Gnomes, ROck Monsters And Chili Sauce
:-) VERSION 4.0.5 (-:
Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2008, The GROMACS development team,
check out http://www.gromacs.org for more information.
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License
as published by the Free Software Foundation; either version 2
of the License, or (at your option) any later version.
:-) genbox_d (double precision) (-:
Option Filename Type Description
------------------------------------------------------------
-cp Complex.pdb Input, Opt! Structure file: gro g96 pdb tpr tpb tpa
-cs ffamber_tip3p.gro Input, Opt!, Lib. Structure file: gro g96 pdb tpr tpb
tpa
-ci insert.gro Input, Opt. Structure file: gro g96 pdb tpr tpb tpa
-o Complex_b4ion.pdb Output Structure file: gro g96 pdb
-p Complex.top In/Out, Opt! Topology file
Option Type Value Description
------------------------------------------------------
-[no]h bool no Print help info and quit
-nice int 19 Set the nicelevel
-box vector 0 0 0 box size
-nmol int 0 no of extra molecules to insert
-try int 10 try inserting -nmol*-try times
-seed int 1997 random generator seed
-vdwd real 0.105 default vdwaals distance
-shell real 0 thickness of optional water layer around solute
-maxsol int 0 maximum number of solvent molecules to add if
they fit in the box. If zero (default) this is
ignored
-[no]vel bool no keep velocities from input solute and solvent
Opening library file /usr/local/gromacs/share/gromacs/top/aminoacids.dat
Opening library file /usr/local/gromacs/share/gromacs/top/atommass.dat
Opening library file /usr/local/gromacs/share/gromacs/top/vdwradii.dat
Opening library file /usr/local/gromacs/share/gromacs/top/dgsolv.dat
Opening library file /usr/local/gromacs/share/gromacs/top/electroneg.dat
Opening library file /usr/local/gromacs/share/gromacs/top/elements.dat
Reading solute configuration
Gnomes, ROck Monsters And Chili Sauce
Containing 3911 atoms in 245 residues
Initialising van der waals distances...
Reading solvent configuration
"TIP3P "
solvent configuration contains 1536 atoms in 512 residues
Initialising van der waals distances...
Will generate new solvent configuration of 4x3x3 boxes
Generating configuration
Sorting configuration
Found 1 molecule type:
SOL ( 3 atoms): 18432 residues
Calculating Overlap...
box_margin = 0.315
Removed 13545 atoms that were outside the box
Succesfully made neighbourlist
nri = 83551, nrj = 2569378
Checking Protein-Solvent overlap: tested 74778 pairs, removed 3885 atoms.
Checking Solvent-Solvent overlap: tested 397797 pairs, removed 4941 atoms.
Added 10975 molecules
Generated solvent containing 32925 atoms in 10975 residues
Writing generated configuration to Complex_b4ion.pdb
Gnomes, ROck Monsters And Chili Sauce
Output configuration contains 36836 atoms in 11220 residues
Volume : 370.58 (nm^3)
Density : 1342.42 (g/l)
Number of SOL molecules: 10975
Processing topology
Back Off! I just backed up Complex.top to ./#Complex.top.1#
gcq#260: "I Quit My Job Blowing Leaves" (Beck)
WARNING: masses will be determined based on residue and atom names,
this can deviate from the real mass of the atom type
Entries in atommass.dat: 178
WARNING: vdwradii will be determined based on residue and atom names,
this can deviate from the real mass of the atom type
Entries in vdwradii.dat: 29
Entries in dgsolv.dat: 7
Entries in electroneg.dat: 71
Entries in elements.dat: 218
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: 22 x 18 x 15 cells
Adding line for 10975 solvent molecules to topology file (Complex.top)
grompp_d -f em.mdp -c Complex_b4ion.pdb -p Complex.top -o Complex_b4ion.tpr
Option Filename Type Description
------------------------------------------------------------
-f em.mdp Input, Opt! grompp input file with MD parameters
-po mdout.mdp Output grompp input file with MD parameters
-c Complex_b4ion.pdb Input Structure file: gro g96 pdb tpr tpb tpa
-r conf.gro Input, Opt. Structure file: gro g96 pdb tpr tpb tpa
-rb conf.gro Input, Opt. Structure file: gro g96 pdb tpr tpb tpa
-n index.ndx Input, Opt. Index file
-p Complex.top Input Topology file
-pp processed.top Output, Opt. Topology file
-o Complex_b4ion.tpr Output Run input file: tpr tpb tpa
-t traj.trr Input, Opt. Full precision trajectory: trr trj cpt
-e ener.edr Input, Opt. Energy file: edr ene
Option Type Value Description
------------------------------------------------------
-[no]h bool no Print help info and quit
-nice int 0 Set the nicelevel
-[no]v bool yes Be loud and noisy
-time real -1 Take frame at or first after this time.
-[no]rmvsbds bool yes Remove constant bonded interactions with virtual
sites
-maxwarn int 0 Number of allowed warnings during input processing
-[no]zero bool no Set parameters for bonded interactions without
defaults to zero instead of generating an error
-[no]renum bool yes Renumber atomtypes and minimize number of
atomtypes
checking input for internal consistency...
Opening library file /usr/local/gromacs/share/gromacs/top/ffamber99sb.itp
Opening library file /usr/local/gromacs/share/gromacs/top/ffamber99sbnb.itp
Opening library file /usr/local/gromacs/share/gromacs/top/ffamber99sbbon.itp
Generated 3403 of the 3403 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 0.5
Generated 3403 of the 3403 1-4 parameter combinations
Opening library file /usr/local/gromacs/share/gromacs/top/spce.itp
-------------------------------------------------------
Program grompp_d, VERSION 4.0.5
Source code file: toppush.c, line: 1273
Fatal error:
[ file spce.itp, line 32 ]:
Atom index (1) in bonds out of bounds (1-0).
This probably means that you have inserted topology section "bonds"
in a part belonging to a different molecule than you intended to.
In that case move the "bonds" section to the right molecule.
-------------------------------------------------------
"I Quit My Job Blowing Leaves" (Beck)
:-) G R O M A C S (-:
God Rules Over Mankind, Animals, Cosmos and Such
:-) VERSION 4.0.5 (-:
Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2008, The GROMACS development team,
check out http://www.gromacs.org for more information.
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License
as published by the Free Software Foundation; either version 2
of the License, or (at your option) any later version.
:-) grompp_d (double precision) (-:
processing topology...
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