[gmx-users] using Berger Lipids in gromacs 4.5.3

Justin A. Lemkul jalemkul at vt.edu
Tue Jan 25 01:48:52 CET 2011


The issue is in atomtypes.atp and is related to an open issue:

http://redmine.gromacs.org/issues/618

Something is wrong with the way atomtypes.atp is handled, such that if any 
change is made to it, pdb2gmx either hangs or assigns the wrong atom types.

There is no need to modify the .atp file for the force field.  Deleting the 
lines you added (and the blank at the end of the file, which in and of itself 
causes a hang) fixes the problem.

-Justin

NG HUI WEN wrote:
> Sorry! Was quite sure I had them attached...
> 
> Thanks again!!
> 
> Huiwen
> 
> -----Original Message-----
> From: Justin A. Lemkul [mailto:jalemkul at vt.edu] 
> Sent: Tuesday, January 25, 2011 8:27 AM
> To: NG HUI WEN
> Subject: Re: [gmx-users] using Berger Lipids in gromacs 4.5.3
> 
> 
> There is no attachment.
> 
> -Justin
> 
> NG HUI WEN wrote:
>> Hi Justin,
>>
>> Here are the files for you. Many thanks for your help in advance!
>> Let me know if you need anything else.
>>
>> Huiwen
>>
>>
>> -----Original Message-----
>> From: gmx-users-bounces at gromacs.org on behalf of Justin A. Lemkul
>> Sent: Mon 1/24/2011 10:48 PM
>> To: Gromacs Users' List
>> Subject: Re: [gmx-users] using Berger Lipids in gromacs 4.5.3
>>  
>>
>>
>> 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
>>>>>
>>>>>
>>>>>
>>>>> <<
>>>>>
>>>>> This message and any attachment are intended solely for the addressee and
>>>>> may contain confidential information. If you have received this message
>>>>> in error, please send it back to me, and immediately delete it. Please do
>>>>> not use, copy or disclose the information contained in this message or in
>>>>> any attachment. Any views or opinions expressed by the author of this
>>>>> email do not necessarily reflect the views of the University of
>>>>> Nottingham.
>>>>>
>>>>> This message has been checked for viruses but the contents of an 
>>>>> attachment may still contain software viruses which could damage your 
>>>>> computer system: you are advised to perform your own checks. Email 
>>>>> communications with the University of Nottingham may be monitored as 
>>>>> permitted by UK & Malaysia legislation.
>>>>>
>>>>> <<
>>>>>
>>>>> This message and any attachment are intended solely for the addressee and
>>>>> may contain confidential information. If you have received this message
>>>>> in error, please send it back to me, and immediately delete it. Please do
>>>>> not use, copy or disclose the information contained in this message or in
>>>>> any attachment. Any views or opinions expressed by the author of this
>>>>> email do not necessarily reflect the views of the University of
>>>>> Nottingham.
>>>>>
>>>>> This message has been checked for viruses but the contents of an 
>>>>> attachment may still contain software viruses which could damage your 
>>>>> computer system: you are advised to perform your own checks. Email 
>>>>> communications with the University of Nottingham may be monitored as 
>>>>> permitted by UK & Malaysia legislation.
>>>>>
> 

-- 
========================================

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

========================================



More information about the gromacs.org_gmx-users mailing list