[gmx-users] Issue with Atom Types/Charges/Mass when including ATP in gromos53.a6
Thomas Piggot
t.piggot at soton.ac.uk
Wed Sep 22 23:41:25 CEST 2010
Hi,
I am not sure why there is not an error message but something is going
very wrong (from looking at the topology produced by pdb2gmx).
I have had issues (in older versions of GROMACS) where the four letter
naming of atoms for ATP in GROMOS has caused problems. I tried your pdb
with the letter 'A' removed from before all of the atom names and with
the corresponding entries the aminoacids.rtp and aminoacids.hdb files
also updated. With this I get the correct topology.
Again I am not sure why you don't get an error from pdb2gmx, maybe
someone else can comment on this or maybe you should file a bugzilla.
Cheers
Tom
On 22/09/10 17:49, aschug at ctbp.ucsd.edu wrote:
> 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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--
Dr Thomas Piggot
University of Southampton, UK.
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