[gmx-users] SS bridges
Dmitry Kovalsky
dikov at imbg.org.ua
Mon Jul 12 18:30:40 CEST 2004
On Saturday 10 July 2004 17:30, you wrote:
> On Sat, 2004-07-10 at 15:32, Dmitry Kovalsky wrote:
> > Hi there,
> >
> > I have a protein with two chains. There are also lots of intra SS-bridges
> > and one inter SS-bridge. When I invoke pdb2gmx it sems to regognize them
> > properly however in the output gro file the Cys residues are protonated
> > and does not form SS bridges.
> >
> > Usage of -ss option does not allow me to select Cyts residues, it is not
> > interactive!
> >
> > How I can manage this problem?
>
> try pdb2gmx -merge
However there are Cys-Cys bonds within one chain that are not processed
properly also.
Any way I tried -merge and this does not result in merging SS bonds.
Any ideas?
If I manually substitute in top file all CYSH entries with CYS2? Is it a walk
around?
>
> > Here the output of the pdb2gmx
> >
> > [dikov at violet 777]$ pdb2gmx -f 1FJS.pdb -o Xa_SS.pdb -p Xa_SS1 -ignh
> > -ss
> >
> > :-) G R O M A C S (-:
> >
> > S C A M O R G
> >
> > :-) 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 my.pdb Input Generic structure: gro g96 pdb tpr tpb
> > tpa xml
> > -o my_out.pdb Output Generic structure: gro g96 pdb xml
> > -p my.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 yes 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 yes
> > 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)
> > 2
> > Looking whether force field file ffG43a2.rtp exists
> > Opening library file /usr/local/share/gromacs/top/ffG43a2.rtp
> > Opening library file /usr/local/share/gromacs/top/aminoacids.dat
> > Reading my.pdb...
> > Read 'protein', 2401 atoms
> > Opening library file /usr/local/share/gromacs/top/xlateat.dat
> > 23 out of 23 lines of xlateat.dat converted succesfully
> > Analyzing pdb file
> > Gave chain 3 chain identifier 'B'
> > There are 3 chains and 1 blocks of water and 451 residues with 2401 atoms
> >
> > chain #res #atoms
> > 1 'A' 234 1852
> > 2 'L' 52 384
> > 3 'B' 2 2
> > 4 '-' 163 163 (only water)
> >
> > WARNING: there were 14 atoms with zero occupancy and 20 atoms with
> > occupancy unequal to one (out of 2401 atoms). Check your pdb
> > file. Opening library file /usr/local/share/gromacs/top/ffG43a2.atp
> > Atomtype 50
> > Reading residue database... (ffG43a2)
> > Opening library file /usr/local/share/gromacs/top/ffG43a2.rtp
> > Residue 96
> > Sorting it all out...
> > Opening library file /usr/local/share/gromacs/top/ffG43a2.hdb
> > Opening library file /usr/local/share/gromacs/top/ffG43a2-n.tdb
> > Opening library file /usr/local/share/gromacs/top/ffG43a2-c.tdb
> > Processing chain 1 'A' (1852 atoms, 234 residues)
> > Opening library file /usr/local/share/gromacs/top/specbond.dat
> > 5 out of 5 lines of specbond.dat converted succesfully
> > Special Atom Distance matrix:
> > CYS7 CYS12 CYS27 HIS42 CYS43 HIS69 HIS77
> > SG47 SG83 SG206 NE2318 SG324 NE2536 NE2602
> > CYS12 SG83 0.230
> > CYS27 SG206 1.706 1.726
> > HIS42 NE2318 1.948 1.957 0.488
> > CYS43 SG324 1.773 1.764 0.239 0.410
> > HIS69 NE2536 1.872 1.798 1.852 2.279 1.873
> > HIS77 NE2602 2.853 2.730 1.835 1.629 1.597 2.634
> > CYS108 SG856 1.708 1.478 2.379 2.509 2.269 1.937 2.281
> > HIS134 NE21060 1.681 1.881 2.029 2.090 2.189 3.133 3.567
> > CYS156 SG1240 2.410 2.363 2.047 1.668 1.921 3.430 1.943
> > CYS170 SG1351 2.251 2.220 1.931 1.568 1.827 3.346 2.037
> > CYS181 SG1433 1.587 1.712 1.218 1.163 1.340 2.724 2.665
> > HIS189 NE21485 1.407 1.306 1.711 1.594 1.615 2.569 1.992
> > CYS209 SG1644 1.746 1.851 1.264 1.115 1.355 2.864 2.577
> > CYS108 HIS134 CYS156 CYS170 CYS181 HIS189
> > SG856 NE21060 SG1240 SG1351 SG1433 NE21485
> > HIS134 NE21060 3.257
> > CYS156 SG1240 2.566 2.504
> > CYS170 SG1351 2.552 2.275 0.230
> > CYS181 SG1433 2.821 0.954 1.796 1.584
> > HIS189 NE21485 1.569 2.167 1.137 1.054 1.611
> > CYS209 SG1644 2.872 1.111 1.617 1.407 0.237 1.574
> > There are 362 donors and 349 acceptors
> > There are 555 hydrogen bonds
> > Will use HISA for residue 42
> > Will use HISB for residue 69
> > Will use HISB for residue 77
> > Will use HISB for residue 134
> > Will use HISB for residue 189
> > Checking for duplicate atoms....
> > N-terminus: NH3+
> > C-terminus: COO-
> > Now there are 234 residues with 2405 atoms
> > Chain time...
> > Making bonds...
> > Opening library file /usr/local/share/gromacs/top/aminoacids.dat
> > Number of bonds was 2448, now 2443
> > Generating angles, dihedrals and pairs...
> > Before cleaning: 3914 pairs
> > Before cleaning: 4630 dihedrals
> > There are 1273 dihedrals, 1214 impropers, 3560 angles
> > 3914 pairs, 2443 bonds and 0 dummies
> > Total mass 26412.180 a.m.u.
> > Total charge 1.000 e
> > Writing topology
> > Processing chain 2 'L' (384 atoms, 52 residues)
> > Opening library file /usr/local/share/gromacs/top/specbond.dat
> > 5 out of 5 lines of specbond.dat converted succesfully
> > Special Atom Distance matrix:
> > CYS3 CYS10 CYS14 HIS15 CYS23 CYS25 CYS38
> > SG23 SG71 SG105 NE2115 SG176 SG188 SG280
> > CYS10 SG71 0.578
> > CYS14 SG105 0.236 0.347
> > HIS15 NE2115 0.735 0.673 0.662
> > CYS23 SG176 0.752 0.229 0.539 0.710
> > CYS25 SG188 1.344 0.870 1.141 0.855 0.787
> > CYS38 SG280 1.299 0.804 1.083 0.926 0.760 0.239
> > CYS46 SG338 1.943 1.630 1.787 1.458 1.656 0.993 0.967
> >
> >
> > There are 74 donors and 80 acceptors
> > There are 118 hydrogen bonds
> > Will use HISB for residue 15
> > Checking for duplicate atoms....
> > N-terminus: NH3+
> > C-terminus: COO-
> > Now there are 52 residues with 491 atoms
> > Chain time...
> > Making bonds...
> > Opening library file /usr/local/share/gromacs/top/aminoacids.dat
> > Number of bonds was 502, now 497
> > Generating angles, dihedrals and pairs...
> > Before cleaning: 827 pairs
> > Before cleaning: 923 dihedrals
> > There are 275 dihedrals, 226 impropers, 718 angles
> > 827 pairs, 497 bonds and 0 dummies
> > Total mass 5581.227 a.m.u.
> > Total charge -3.000 e
> > Writing topology
> > Processing chain 3 'B' (2 atoms, 2 residues)
> > Opening library file /usr/local/share/gromacs/top/specbond.dat
> > 5 out of 5 lines of specbond.dat converted succesfully
> > There are 0 donors and 0 acceptors
> > There are 0 hydrogen bonds
> > Warning: 'CA' not found in residue topology database, trying to use
> > 'CA2+' Warning: 'CL' not found in residue topology database, trying to
> > use 'CL-' Checking for duplicate atoms....
> > No N- or C-terminus found: this chain appears to contain no protein
> > Now there are 2 residues with 2 atoms
> > Chain time...
> > Warning: 'CA' not found in residue topology database, trying to use
> > 'CA2+' Warning: 'CL' not found in residue topology database, trying to
> > use 'CL-' Making bonds...
> > Opening library file /usr/local/share/gromacs/top/aminoacids.dat
> > No bonds
> > Generating angles, dihedrals and pairs...
> > There are 0 dihedrals, 0 impropers, 0 angles
> > 0 pairs, 0 bonds and 0 dummies
> > Total mass 75.533 a.m.u.
> > Total charge 1.000 e
> > Writing topology
> > Processing chain 4 (163 atoms, 163 residues)
> > Opening library file /usr/local/share/gromacs/top/specbond.dat
> > 5 out of 5 lines of specbond.dat converted succesfully
> > There are 163 donors and 163 acceptors
> > There are 39 hydrogen bonds
> > Checking for duplicate atoms....
> > Now there are 163 residues with 489 atoms
> > Making bonds...
> > Opening library file /usr/local/share/gromacs/top/aminoacids.dat
> > Number of bonds was 489, now 489
> > Generating angles, dihedrals and pairs...
> > There are 0 dihedrals, 0 impropers, 489 angles
> > 0 pairs, 489 bonds and 0 dummies
> > Total mass 2936.510 a.m.u.
> > Total charge 0.000 e
> > Including chain 1 in system: 2405 atoms 234 residues
> > Including chain 2 in system: 491 atoms 52 residues
> > Including chain 3 in system: 2 atoms 2 residues
> > Including chain 4 in system: 489 atoms 163 residues
> > Now there are 3387 atoms and 451 residues
> > Total mass in system 35005.450 a.m.u.
> > Total charge in system -1.000 e
> >
> > Writing coordinate file...
> > --------- PLEASE NOTE ------------
> > You have succesfully generated a topology from: my.pdb.
> > The select force field and the spc 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#206: "I Do It All the Time" (Magnapop)
> >
> >
> > Thanks in advance
--
Sincerely yours,
Ph.D. Student Dmytro Kovalskyy
Institute of Molecular Biology & Genetics
150 Akad. Zabolotnogo Street,
Kiev-143, 03143
UKRAINE
E-mail: dikov at imbg.org.ua
Fax: +380 (44) 266-0759
Tel.: +380 (44) 266-5589
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