[gmx-users] using Berger Lipids in gromacs 4.5.3
Justin A. Lemkul
jalemkul at vt.edu
Sun Jan 23 14:05:52 CET 2011
NG HUI WEN wrote:
> Oops sorry!
>
> I found the mistake...
>
> the topology file should read
> "gromos53a6_lipid.ff/forcefield.itp" instead of
> "gromos53a6.ff/forcefield.itp"
>
You would have gotten this if you had chosen the proper force field with
pdb2gmx. Option 1 (which includes the Berger lipids) is the correct one.
Option 14 is the vanilla Gromos96 53a6 force field, which is not what you want.
-Justin
> silly me
>
> ------------------------------------------------------------------------
> *From:* gmx-users-bounces at gromacs.org on behalf of NG HUI WEN
> *Sent:* Sun 1/23/2011 1:40 PM
> *To:* gmx-users at gromacs.org
> *Subject:* [gmx-users] using Berger Lipids in gromacs 4.5.3
>
> Dear all,
>
> This must be a pretty simple problem but I am stuck nonetheless. I have
> been using the lipids from Prof Tieleman's website without any problem
> on gromacs 4.0.7.
>
> Now that I've got 4.5.3 installed, I want to try the g_membed tool but
> have encountered these problems.
>
> Following Justin's tutorial which gives a good tip on how to deal with
> the changes introduced in 4.5.3, these are the things I have done + the
> output
>
> 1) gave new names to the modified itp files from 4.0.7
> ffG53a6_lipid.itp to forcefield.itp
> ffG53a6nb_lipid.itp to ffnonbonded.itp
> ffG53a6bon_lipid.itp to ffbonded.itp
>
> 2) created a folder gromos53a6_lipid.ff in the working directory to
> contain the files in (1)
>
> 3) copied aminoacids.c.tdb, aminoacids.n.tdb, aminoacids.hdb,
> aminoacids.r2b, aminoacids.rtp, aminoacids.vsd, ff_dumitp, spc.itp,
> ions.itp, watermodels.dat from $GMXLIB into the gromos53a6_lipid.ff
> folder created in step (2). The created a forcefield.doc as instructed.
>
> 4) created .itp for my protein with pdb2gmx
> huiwen3 at magnum <mailto:huiwen3 at magnum> 182% pdb2gmx -f protein_moved.pdb
> -o protein_pdb2gmx.pdb -p protein.top -ignh
> :-) G R O M A C S (-:
> Giant Rising Ordinary Mutants for A Clerical Setup
> :-) VERSION 4.5.3 (-:
> 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, Pieter Meulenhoff,
> Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schulz,
> 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 <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 protein_moved.pdb Input Structure file: gro g96 pdb tpr etc.
> -o protein_pdb2gmx.pdb Output Structure file: gro g96 pdb etc.
> -p protein.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 select Force field, interactive by default. Use -h for
> information.
> -water enum select 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 no 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
>
> Select the Force Field:
> From current directory:
> 1: GROMOS96 53A6 force field, extended to include Berger lipid parameters
> From '/usr/remote/gromacs/4.5.3/share/gromacs/top':
> 2: AMBER03 force field (Duan et al., J. Comp. Chem. 24, 1999-2012, 2003)
> 3: AMBER94 force field (Cornell et al., JACS 117, 5179-5197, 1995)
> 4: AMBER96 force field (Kollman et al., Acc. Chem. Res. 29, 461-469, 1996)
> 5: AMBER99 force field (Wang et al., J. Comp. Chem. 21, 1049-1074, 2000)
> 6: AMBER99SB force field (Hornak et al., Proteins 65, 712-725, 2006)
> 7: AMBER99SB-ILDN force field (Lindorff-Larsen et al., Proteins 78,
> 1950-58, 2010)
> 8: AMBERGS force field (Garcia & Sanbonmatsu, PNAS 99, 2782-2787, 2002)
> 9: CHARMM27 all-atom force field (with CMAP) - version 2.0
> 10: GROMOS96 43a1 force field
> 11: GROMOS96 43a2 force field (improved alkane dihedrals)
> 12: GROMOS96 45a3 force field (Schuler JCC 2001 22 1205)
> 13: GROMOS96 53a5 force field (JCC 2004 vol 25 pag 1656)
> 14: GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656)
> 15: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)
> 16: [DEPRECATED] Encad all-atom force field, using full solvent charges
> 17: [DEPRECATED] Encad all-atom force field, using scaled-down vacuum
> charges
> 18: [DEPRECATED] Gromacs force field (see manual)
> 19: [DEPRECATED] Gromacs force field with hydrogens for NMR
> I selected 14 ....
> Q: should I pick 1 instead?
> 5) combined protein and lipid structure files with cat protein_moved.pdb
> popc_solvated.pdb > merged.pdb, deleted some uneccessary lines
> and changed CRYST1 to that of the lipid
>
> 6) Obtained a sample.mdp file from
> http://wwwuser.gwdg.de/~ggroenh/membed.html called it g_membed_sample.mdp
>
> 7) did grompp -f sample.mdp -c merged.pdb -p merged.top -o input.tpr and
> got this error
> :-) G R O M A C S (-:
> Giant Rising Ordinary Mutants for A Clerical Setup
> :-) VERSION 4.5.3 (-:
> 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, Pieter Meulenhoff,
> Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schulz,
> 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 <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.
> :-) grompp (-:
> Option Filename Type Description
> ------------------------------------------------------------
> -f g_membed_sample.mdp Input grompp input file with MD parameters
> -po mdout.mdp Output grompp input file with MD parameters
> -c merged.pdb Input Structure file: gro g96 pdb tpr etc.
> -r conf.gro Input, Opt. Structure file: gro g96 pdb tpr etc.
> -rb conf.gro Input, Opt. Structure file: gro g96 pdb tpr etc.
> -n index.ndx Input, Opt. Index file
> -p merged.top Input Topology file
> -pp processed.top Output, Opt. Topology file
> -o input.tpr Output Run input file: tpr tpb tpa
> -t traj.trr Input, Opt. Full precision trajectory: trr trj cpt
> -e ener.edr Input, Opt. Energy file
> 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
> -[no]v bool no Be loud and noisy
> -time real -1 Take frame at or first after this time.
> -[no]rmvsbds bool yes Remove constant bonded interactions with virtual
> sites
> -maxwarn int 0 Number of allowed warnings during input
> processing
> -[no]zero bool no Set parameters for bonded interactions without
> defaults to zero instead of generating an error
> -[no]renum bool yes Renumber atomtypes and minimize number of
> atomtypes
>
> Back Off! I just backed up mdout.mdp to ./#mdout.mdp.3#
> NOTE 1 [file g_membed_sample.mdp]:
> nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
> nstcomm to nstcalcenergy
> Generated 165 of the 1596 non-bonded parameter combinations
> -------------------------------------------------------
> Program grompp, VERSION 4.5.3
> Source code file: toppush.c, line: 1166
> Fatal error:
> Atomtype LC3 not found
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> -------------------------------------------------------
> "Your Country Needs YOU" (U.S. Army)
>
> 8) My merged.top looks like this
>
> ; Include forcefield parameters
> #include "gromos53a6.ff/forcefield.itp"
>
> ;Include Protein Topology
> #include "protein.itp"
>
> ; Include Position restraint file
> #ifdef POSRES
> #include "posre.itp"
> #endif
> ;
> ;
> ;Include POPC topology
> #include "popc.itp"
> ;
> ;Include water topology
> #include "gromos53a6.ff/spc.itp"
>
> #ifdef POSRES_WATER
> ; Position restraint for each water oxygen
> [ position_restraints ]
> ; i funct fcx fcy fcz
> 1 1 1000 1000 1000
> #endif
>
> ; Include topology for ions
> #include "gromos53a6.ff/ions.itp"
>
> [ system ]
> ; Name
> POPC in water + Protein
>
> [ molecules ]
> ; Compound #mols
> Protein_X 1
> POPC 339
> SOL 16865
> I am certain I have LC3 in the ffnonbonded.itp file I created in step
> (1)...
>
> Many thanks for your help in advance.
>
> Huiwen
>
>
>
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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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