[gmx-users] Fatal error
Anthony Cruz
acb15885 at uprm.edu
Mon Jan 30 23:59:29 CET 2006
Hi Users:
I am trying to run a simulation of a hemeprotein with cn bounded. I edit the
specbond.dat to include the cyanide ion and link it to the heme FE after that
I include the necesary bond parameters in the ff*bon.itp and include CYN
residue in the ff*.rtp. When I run pdb2gmx the program stop with the followin
erro:
:-) G R O M A C S (-:
Good ROcking Metal Altar for Chronical Sinners
:-) VERSION 3.2.1 (-:
Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2004, 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 (-:
Option Filename Type Description
------------------------------------------------------------
-f 1B0B.pdb Input Generic structure: gro g96 pdb tpr tpb tpa
xml
-o conf.gro Output Generic structure: gro g96 pdb xml
-p topol.top Output Topology file
-i posre.itp Output Include file for topology
-n clean.ndx Output, Opt. Index file
-q clean.pdb Output, Opt. Generic structure: gro g96 pdb xml
Option Type Value Description
------------------------------------------------------
-[no]h bool no Print help info and quit
-nice int 0 Set the nicelevel
-[no]merge bool no Merge multiple chains into one molecule
-ff string select Force field, interactive by default. Use -h for
information.
-water enum spc Water model to use: with GROMOS we recommend SPC,
with OPLS, TIP4P: spc, spce, tip3p, tip4p or
tip5p
-[no]inter bool no Set the next 6 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]asp bool no Interactive Aspartic Acid selection, iso charged
-[no]glu bool no Interactive Glutamic Acid selection, iso charged
-[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 no Ignore hydrogen atoms that are in the pdb file
-[no]missing bool no Continue when atoms are missing, dangerous
-posrefc real 1000 Force constant for position restraints
-dummy enum none Convert atoms to dummy atoms: 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/share/gromacs/top/FF.dat
Select the Force Field:
0: GROMOS96 43a1 Forcefield (official distribution)
1: GROMOS96 43b1 Vacuum Forcefield (official distribution)
2: GROMOS96 43a2 Forcefield (development) (improved alkane dihedrals)
3: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)
4: Gromacs Forcefield (see manual)
5: gmx Forcefield with hydrogens for NMR stuff (Do NOT use for new runs)
6: AMBER94 Cornell protein/nucleic forcefield (helix-friendly)
7: AMBER96 Kollman protein/nucleic acid forcefield (f/y torsional potentials
- disfavoring helices, favoring extended conformations)
8: AMBER99 Wang protein/nucleic acid forcefield (updates for both amino and
nucleic acids)
9: AMBER99p Sorin & Pande protein/nucleic forcefield (variant for helix-coil
simulations replaces f torsion in AMBER-99 with AMBER-94)
10: AMBERGS Garcia & Sanbonmatsu protein/nucleic (f/y torsional potentials
removed, set to zero)
11: AMBERGSs Nymeyer & Garcia protein/nucleic (*NOT* scale 1-4 vdW
interactions)
0
Looking whether force field file ffG43a1.rtp exists
Opening library file ffG43a1.rtp
Opening library file /usr/local/share/gromacs/top/aminoacids.dat
Reading 1B0B.pdb...
Read 'HEMOGLOBIN', 1304 atoms
Opening library file /usr/local/share/gromacs/top/xlateat.dat
23 out of 23 lines of xlateat.dat converted succesfully
Analyzing pdb file
There are 1 chains and 1 blocks of water and 346 residues with 1304 atoms
chain #res #atoms
1 ' ' 144 1102
2 '-' 202 202 (only water)
WARNING: there were 0 atoms with zero occupancy and 66 atoms with
occupancy unequal to one (out of 1304 atoms). Check your pdb file.
Opening library file ffG43a1.atp
Atomtype 50
Reading residue database... (ffG43a1)
Opening library file ffG43a1.rtp
Residue 97
Sorting it all out...
Opening library file ffG43a1.hdb
Opening library file ffG43a1-n.tdb
Opening library file ffG43a1-c.tdb
Processing chain 1 (1102 atoms, 144 residues)
Opening library file specbond.dat
6 out of 6 lines of specbond.dat converted succesfully
Special Atom Distance matrix:
HIS36 CYS89 HIS96 HEME143 HEME143 HEME143
NE2281 SG672 NE2727 FE1058 CAB1080 CAC1088
CYS89 SG672 1.916
HIS96 NE2727 1.480 1.136
HEME143 FE1058 1.414 1.248 0.213
HEME143 CAB1080 1.171 0.953 0.595 0.552
HEME143 CAC1088 1.066 1.559 0.592 0.560 0.797
CYN144 C1101 1.375 1.361 0.407 0.195 0.569 0.602
Linking HIS-96 NE2-727 and HEME-143 FE-1058...
Linking HEME-143 FE-1058 and CYN-144 C-1101...
There are 202 donors and 200 acceptors
There are 274 hydrogen bonds
Will use HISB for residue 36
Checking for duplicate atoms....
deleting duplicate atom CB LYSH 11 pdb nr 80 altloc B
deleting duplicate atom CG LYSH 11 pdb nr 82 altloc B
deleting duplicate atom CD LYSH 11 pdb nr 84 altloc B
deleting duplicate atom CE LYSH 11 pdb nr 86 altloc B
deleting duplicate atom NZ LYSH 11 pdb nr 88 altloc B
deleting duplicate atom CB SER 12 pdb nr 94 altloc B
deleting duplicate atom OG SER 12 pdb nr 96 altloc B
deleting duplicate atom CB SER 13 pdb nr 102 altloc B
deleting duplicate atom OG SER 13 pdb nr 104 altloc B
deleting duplicate atom CE LYSH 16 pdb nr 132 altloc B
deleting duplicate atom NZ LYSH 16 pdb nr 134 altloc B
deleting duplicate atom CB SER 18 pdb nr 145 altloc B
deleting duplicate atom OG SER 18 pdb nr 147 altloc B
deleting duplicate atom CE LYSH 42 pdb nr 332 altloc B
deleting duplicate atom NZ LYSH 42 pdb nr 334 altloc B
deleting duplicate atom CB VAL 76 pdb nr 581 altloc B
deleting duplicate atom CG1 VAL 76 pdb nr 583 altloc B
deleting duplicate atom CG2 VAL 76 pdb nr 585 altloc B
deleting duplicate atom O MET 142 pdb nr 1060
Now there are 1083 atoms
N-terminus: NH3+
C-terminus: COO-
Fatal error: Atom CA not found in residue CYN144 while adding hydrogens
What could be the problem?? How I could resolve it??
Thanks.
Anthony
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