Dear all,
I want to run some simulations of a kinase with an ATP molecule using
gromacs 4.5.1 with the gromos53a6.ff forcefield. To generate the .gro and
.top files I am running
pdb2gmx -v -f ATP.pdb -p initial.top -o initial.gro -ff gromos53a6 -water spc
Now the generated topology file shows some odd atom types, charges, and
masses which differ from the ones found in the ATP-entry of gromos53a6.ff:
[ atoms ]
; nr type resnr residue atom cgnr charge mass typeB
chargeB massB
1 NR 476 ATP AN9 1 -0.2 14.0067 ;
qtot -0.2
2 O 476 ATP AC4 2 0 1.48594e-41 ;
qtot -0.2
I played a bit with the chain-termini etc. but could not fix the issue and
guess I must be doing some silly mistake. I would therefore greatly
appreciate some help/pointers.
Thank you,
Alex
ps:
##################
ATP.pdb (just the ATP-molecule, when I take the entire complex of protein
structure+ATP I get the same issues)
ATOM 3826 APB ATP D 476 47.748 48.397 59.538 0.00227.61
ATOM 3827 AO3B ATP D 476 47.540 49.729 58.745 0.00227.61
ATOM 3828 AO2B ATP D 476 49.145 48.068 60.002 0.00227.61
ATOM 3829 AO1B ATP D 476 47.038 47.146 58.965 0.00227.61
ATOM 3830 APA ATP D 476 46.063 49.828 61.632 0.00227.61
ATOM 3831 AO1A ATP D 476 44.574 49.457 61.408 0.00227.61
ATOM 3832 AO2A ATP D 476 46.341 51.157 61.156 0.00227.61
ATOM 3833 AO3A ATP D 476 46.956 48.594 60.969 0.00227.61
ATOM 3834 AO5* ATP D 476 46.560 49.512 63.160 0.00227.61
ATOM 3835 AC5* ATP D 476 48.092 49.215 63.245 0.00227.61
ATOM 3836 AC4* ATP D 476 48.454 48.749 64.571 0.00227.61
ATOM 3837 AO4* ATP D 476 47.347 48.436 65.439 0.00227.61
ATOM 3838 AC3* ATP D 476 49.180 47.483 64.374 0.00227.61
ATOM 3839 AO3* ATP D 476 50.540 47.515 64.449 0.00227.61
ATOM 3840 AC2* ATP D 476 48.751 46.656 65.478 0.00227.61
ATOM 3841 AO2* ATP D 476 49.542 46.012 66.564 0.00227.61
ATOM 3842 AC1* ATP D 476 47.572 47.225 66.121 0.00227.61
ATOM 3843 AN9 ATP D 476 46.374 46.469 65.860 0.00227.61
ATOM 3844 AC8 ATP D 476 45.367 46.820 65.035 0.00227.61
ATOM 3845 AN7 ATP D 476 44.404 45.853 64.941 0.00227.61
ATOM 3846 AC5 ATP D 476 44.697 44.807 65.844 0.00227.61
ATOM 3847 AC6 ATP D 476 44.103 43.545 66.341 0.00227.61
ATOM 3848 AN6 ATP D 476 42.813 43.067 65.910 0.00227.61
ATOM 3849 AN1 ATP D 476 45.064 42.708 67.074 0.00227.61
ATOM 3850 AC2 ATP D 476 46.255 43.142 67.280 0.00227.61
ATOM 3851 AN3 ATP D 476 46.786 44.335 66.975 0.00227.61
ATOM 3852 AC4 ATP D 476 46.065 45.198 66.246 0.00227.61
ATOM 3853 APG ATP D 476 47.198 49.717 57.298 0.00227.61
ATOM 3854 AO1G ATP D 476 47.583 50.876 56.391 0.00227.61
ATOM 3855 AO2G ATP D 476 47.441 48.310 56.911 0.00227.61
ATOM 3856 AO3G ATP D 476 45.690 49.283 57.490 0.00227.61
#########################
from initial.top
[ atoms ]
; nr type resnr residue atom cgnr charge mass typeB
chargeB massB
; residue 476 ATP rtp ATP q +0.7
1 NR 476 ATP AN9 1 -0.2 14.0067 ;
qtot -0.2
2 O 476 ATP AC4 2 0 1.48594e-41 ;
qtot -0.2
3 NR 476 ATP AN3 3 -0.36 14.0067 ;
qtot -0.56
4 O 476 ATP AC2 4 0 1.48594e-41 ;
qtot -0.56
5 O 476 ATP AN1 5 0 1.48594e-41 ;
qtot -0.56
6 C 476 ATP AC6 6 0.36 12.011 ;
qtot -0.2
7 NT 476 ATP AN6 7 -0.83 14.0067 ;
qtot -1.03
8 H 476 ATP AH61 7 0.415 1.008 ;
qtot -0.615
9 H 476 ATP AH62 7 0.415 1.008 ;
qtot -0.2
10 O 476 ATP AC5 8 0 1.48594e-41 ;
qtot -0.2
11 NR 476 ATP AN7 9 -0.36 14.0067 ;
qtot -0.56
12 O 476 ATP AC8 10 0 1.48594e-41 ;
qtot -0.56
13 O 476 ATP AC1* 11 0 1.48594e-41 ;
qtot -0.56
14 OA 476 ATP AO4* 12 -0.36 15.9994 ;
qtot -0.92
15 CH1 476 ATP AC4* 12 0.16 13.019 ;
qtot -0.76
16 O 476 ATP AC2* 13 0 1.48594e-41 ;
qtot -0.76
17 OA 476 ATP AO2* 14 -0.548 15.9994 ;
qtot -1.308
18 H 476 ATP AH2* 14 0.398 1.008 ;
qtot -0.91
19 O 476 ATP AC3* 15 0 1.48594e-41 ;
qtot -0.91
20 OA 476 ATP AO3* 16 -0.548 15.9994 ;
qtot -1.458
21 H 476 ATP AH3* 16 0.398 1.008 ;
qtot -1.06
22 O 476 ATP AC5* 17 0 1.48594e-41 ;
qtot -1.06
23 O 476 ATP AO5* 18 0 1.48594e-41 ;
qtot -1.06
24 O 476 ATP APA 19 0 1.48594e-41 ;
qtot -1.06
25 O 476 ATP AO1A 20 0 1.48594e-41 ;
qtot -1.06
26 O 476 ATP AO2A 21 0 1.48594e-41 ;
qtot -1.06
27 O 476 ATP AO3A 22 0 1.48594e-41 ;
qtot -1.06
28 P 476 ATP APB 23 0.705 30.9738 ;
qtot -0.355
29 O 476 ATP AO1B 24 0 1.48594e-41 ;
qtot -0.355
30 O 476 ATP AO2B 25 0 1.48594e-41 ;
qtot -0.355
31 O 476 ATP AO3B 26 0 1.48594e-41 ;
qtot -0.355
32 P 476 ATP APG 27 0.63 30.9738 ;
qtot 0.275
33 O 476 ATP AO1G 28 0 1.48594e-41 ;
qtot 0.275
34 O 476 ATP AO2G 29 0 1.48594e-41 ;
qtot 0.275
35 O 476 ATP AO3G 30 0 1.48594e-41 ;
qtot 0.275
36 H 476 ATP AH3G 31 0.398 1.008 ;
qtot 0.673
##########################
from gromos53a6.ff/aminoacids.rtp
[ ATP ]
[ atoms ]
AN9 NR -0.20000 0
AC4 C 0.20000 0
AN3 NR -0.36000 1
AC2 CR1 0.36000 1
AN1 NR -0.36000 2
AC6 C 0.36000 2
AN6 NT -0.83000 3
AH61 H 0.41500 3
AH62 H 0.41500 3
AC5 C 0.00000 4
AN7 NR -0.36000 4
AC8 CR1 0.36000 4
AC1* CH1 0.20000 5
AO4* OA -0.36000 5
AC4* CH1 0.16000 5
AC2* CH1 0.15000 6
AO2* OA -0.54800 6
AH2* H 0.39800 6
AC3* CH1 0.15000 7
AO3* OA -0.54800 7
AH3* H 0.39800 7
AC5* CH2 0.00000 8
AO5* OA -0.36000 9
APA P 0.70500 9
AO1A OM -0.63500 9
AO2A OM -0.63500 9
AO3A OA -0.36000 10
APB P 0.70500 10
AO1B OM -0.63500 10
AO2B OM -0.63500 10
AO3B OA -0.36000 11
APG P 0.63000 11
AO1G OM -0.63500 11
AO2G OM -0.63500 11
AO3G OA -0.54800 11
AH3G H 0.39800 11
##############################
pdb2gmx -v -f ATP.pdb -p initial.top -o initial.gro -ff gromos53a6 -water
spc -ignh
:-) G R O M A C S (-:
Glycine aRginine prOline Methionine Alanine Cystine Serine
:-) VERSION 4.5.1 (-:
Written by Emile Apol, Rossen Apostolov, Herman J.C. Berendsen,
Aldert van Buuren, Pär Bjelkmar, Rudi van Drunen, Anton Feenstra,
Gerrit Groenhof, Peter Kasson, Per Larsson, Peiter Meulenhoff,
Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schultz,
Michael Shirts, Alfons Sijbers, Peter Tieleman,
Berk Hess, David van der Spoel, and Erik Lindahl.
Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2010, The GROMACS development team at
Uppsala University & The Royal Institute of Technology, Sweden.
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 ATP.pdb Input Structure file: gro g96 pdb tpr etc.
-o initial.gro Output Structure file: gro g96 pdb etc.
-p initial.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 etc.
Option Type Value Description
------------------------------------------------------
-[no]h bool no Print help info and quit
-[no]version bool no Print version info and quit
-nice int 0 Set the nicelevel
-chainsep enum id_or_ter Condition in PDB files when a new chain and
molecule_type should be started: id_or_ter,
id_and_ter, ter, id or interactive
-ff string gromos53a6 Force field, interactive by default. Use -h
for information.
-water enum spc Water model to use: select, none, spc, spce,
tip3p, tip4p or tip5p
-[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 yes 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
-[no]chargegrp bool yes Use charge groups in the rtp file
-[no]cmap bool yes Use cmap torsions (if enabled in the rtp file)
-[no]renum bool no Renumber the residues consecutively in the output
-[no]rtpres bool no Use rtp entry names as residue names
Using the Gromos53a6 force field in directory gromos53a6.ff
Opening force field file
/usr/local/gromacs/share/gromacs/top/gromos53a6.ff/aminoacids.r2b
Reading ATP.pdb...
Read 31 atoms
Analyzing pdb file
Splitting PDB chains based on TER records or changing chain id.
There are 1 chains and 0 blocks of water and 476 residues with 31 atoms
chain #res #atoms
1 'D' 1 31
Occupancy for atom ATP476-APB is 0.000000 rather than 1
Occupancy for atom ATP476-AO3B is 0.000000 rather than 1
Occupancy for atom ATP476-AO2B is 0.000000 rather than 1
Occupancy for atom ATP476-AO1B is 0.000000 rather than 1
Occupancy for atom ATP476-APA is 0.000000 rather than 1
Occupancy for atom ATP476-AO1A is 0.000000 rather than 1
Occupancy for atom ATP476-AO2A is 0.000000 rather than 1
Occupancy for atom ATP476-AO3A is 0.000000 rather than 1
Occupancy for atom ATP476-AO5* is 0.000000 rather than 1
Occupancy for atom ATP476-AC5* is 0.000000 rather than 1
Occupancy for atom ATP476-AC4* is 0.000000 rather than 1
Occupancy for atom ATP476-AO4* is 0.000000 rather than 1
Occupancy for atom ATP476-AC3* is 0.000000 rather than 1
Occupancy for atom ATP476-AO3* is 0.000000 rather than 1
Occupancy for atom ATP476-AC2* is 0.000000 rather than 1
Occupancy for atom ATP476-AO2* is 0.000000 rather than 1
Occupancy for atom ATP476-AC1* is 0.000000 rather than 1
Occupancy for atom ATP476-AN9 is 0.000000 rather than 1
Occupancy for atom ATP476-AC8 is 0.000000 rather than 1
Occupancy for atom ATP476-AN7 is 0.000000 rather than 1
Occupancy for atom ATP476-AC5 is 0.000000 rather than 1
Occupancy for atom ATP476-AC6 is 0.000000 rather than 1
Occupancy for atom ATP476-AN6 is 0.000000 rather than 1
Occupancy for atom ATP476-AN1 is 0.000000 rather than 1
Occupancy for atom ATP476-AC2 is 0.000000 rather than 1
Occupancy for atom ATP476-AN3 is 0.000000 rather than 1
Occupancy for atom ATP476-AC4 is 0.000000 rather than 1
Occupancy for atom ATP476-APG is 0.000000 rather than 1
Occupancy for atom ATP476-AO1G is 0.000000 rather than 1
Occupancy for atom ATP476-AO2G is 0.000000 rather than 1
Occupancy for atom ATP476-AO3G is 0.000000 rather than 1
All occupancy fields zero. This is probably not an X-Ray structure
Opening force field file
/usr/local/gromacs/share/gromacs/top/gromos53a6.ff/atomtypes.atp
Atomtype 1
Reading residue database... (gromos53a6)
Opening force field file
/usr/local/gromacs/share/gromacs/top/gromos53a6.ff/aminoacids.rtp
Using default: not generating all possible dihedrals
Using default: excluding 3 bonded neighbors
Using default: generating 1,4 H--H interactions
Using default: removing impropers on same bond as a proper
Residue 108
Sorting it all out...
Opening force field file
/usr/local/gromacs/share/gromacs/top/gromos53a6.ff/aminoacids.hdb
Opening force field file
/usr/local/gromacs/share/gromacs/top/gromos53a6.ff/aminoacids.n.tdb
Opening force field file
/usr/local/gromacs/share/gromacs/top/gromos53a6.ff/aminoacids.c.tdb
Processing chain 1 'D' (31 atoms, 1 residues)
There are 0 donors and 0 acceptors
There are 0 hydrogen bonds
Warning: Starting residue ATP476 in chain not identified as Protein/RNA/DNA.
Problem with chain definition, or missing terminal residues.
This chain does not appear to contain a recognized chain molecule.
If this is incorrect, you can edit residuetypes.dat to modify the behavior.
8 out of 8 lines of specbond.dat converted successfully
Checking for duplicate atoms....
Now there are 1 residues with 36 atoms
Making bonds...
Number of bonds was 38, now 38
Generating angles, dihedrals and pairs...
Before cleaning: 42 pairs
Before cleaning: 80 dihedrals
Making cmap torsions...There are 34 dihedrals, 20 impropers, 58 angles
42 pairs, 38 bonds and 0 virtual sites
Total mass 196.043 a.m.u.
Total charge 0.673 e
Writing topology
Writing coordinate file...
--------- PLEASE NOTE ------------
You have successfully generated a topology from: ATP.pdb.
The Gromos53a6 force field and the spc water model are used.
--------- ETON ESAELP ------------
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