[gmx-users] using Berger Lipids in gromacs 4.5.3
Justin A. Lemkul
jalemkul at vt.edu
Mon Jan 24 15:48:17 CET 2011
NG HUI WEN wrote:
> Hi Justin,
>
> Thanks for your reply. I am using linux on a cluster remotely. It is made up
> of Hewlett Packard ProLiant DL160 compute nodes. I didn't see any "._"
> appearing in my gromos53a6_lipid.ff folder.
Can you send me a tarball of your gromos53a6_lipid.ff folder (off-list) so I can
try to troubleshoot this? Your input .pdb file would be useful, as well.
-Justin
>
> Huiwen
>
> -----Original Message----- From: gmx-users-bounces at gromacs.org
> [mailto:gmx-users-bounces at gromacs.org] On Behalf Of Justin A. Lemkul Sent:
> Monday, January 24, 2011 10:14 PM To: Gromacs Users' List Subject: Re:
> [gmx-users] using Berger Lipids in gromacs 4.5.3
>
>
>
> NG HUI WEN wrote:
>> Dear Justin,
>>
>> Thanks for pointing out :) much appreciated.
>>
>> I tried selecting "1" and the process seemed to stop after the work
>> "Atomtype 1", please see below:
>>
>> pdb2gmx -f prot_moved.pdb -o prot_pdb2gmx.pdb -p prot.top -ter -asp -his
>> :-) G R O M A C S (-:
>>
>> GROningen MAchine for Chemical Simulation
>>
>> :-) 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 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
>> prot_moved.pdb Input Structure file: gro g96 pdb tpr etc. -o
>> prot_pdb2gmx.pdb Output Structure file: gro g96 pdb etc. -p
>> prot.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 yes 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 yes 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 yes 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 no 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 1
>>
>> Using the Gromos53a6_lipid force field in directory ./gromos53a6_lipid.ff
>>
>> Opening force field file ./gromos53a6_lipid.ff/watermodels.dat
>>
>> Select the Water Model: 1: SPC simple point charge, recommended 2: SPC/E
>> extended simple point charge 3: None 1 Opening force field file
>> ./gromos53a6_lipid.ff/aminoacids.r2b Reading prot_moved.pdb... Read 4914
>> 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 310
>> residues with 4914 atoms
>>
>> chain #res #atoms 1 'X' 310 4914
>>
>> All occupancies are one Opening force field file
>> ./gromos53a6_lipid.ff/atomtypes.atp Atomtype 1
>>
>> Not sure what happened... Since there is an option "1" available now, do I
>> still need the gromos53a6_lipid.ff in my current working directory?
>>
>
> The only reason that option "1" appeared is because it is in the working
> directory.
>
> What type of machine are you on? I've had this hang happen on my Mac before,
> due to the presence of ._ files when you copy from a different location.
> I've disabled that option on my workstation. Other than that, I have no clue
> why it would stop there.
>
> -Justin
>
>> Thanks a lot!
>>
>> HW
>>
>>
>> -----Original Message----- From: gmx-users-bounces at gromacs.org
>> [mailto:gmx-users-bounces at gromacs.org] On Behalf Of Justin A. Lemkul Sent:
>> Sunday, January 23, 2011 9:06 PM To: Discussion list for GROMACS users
>> Subject: Re: [gmx-users] using Berger Lipids in gromacs 4.5.3
>>
>>
>>
>> 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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>>>>>
>>> <<
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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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