silly me
------------------------------------------------------------------------
*From:* [email protected] on behalf of NG HUI WEN *Sent:* Sun
1/23/2011 1:40 PM *To:* [email protected] *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@magnum
<mailto:huiwen3@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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email do not necessarily reflect the views of the University of
Nottingham.
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