[gmx-users] SS bridges
David
spoel at xray.bmc.uu.se
Sat Jul 10 16:30:32 CEST 2004
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
>
> 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
--
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
spoel at xray.bmc.uu.se spoel at gromacs.org http://xray.bmc.uu.se/~spoel
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