[gmx-users] SS bridges
Dmitry Kovalsky
dikov at imbg.org.ua
Sat Jul 10 15:32:01 CEST 2004
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?
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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