[gmx-users] using Berger Lipids in gromacs 4.5.3
NG HUI WEN
HuiWen.Ng at nottingham.edu.my
Sun Jan 23 07:05:45 CET 2011
Oops sorry!
I found the mistake...
the topology file should read
"gromos53a6_lipid.ff/forcefield.itp" instead of "gromos53a6.ff/forcefield.itp"
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 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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