[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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