RE: [gmx-users] using Berger Lipids in gromacs 4.5.3

[NG HUI WEN]

It worked! Thanks very much again for your time and help.

Cheers,
huiwen

-Original Message-
From: Justin A. Lemkul [mailto:jalem...@vt.edu] 
Sent: Tuesday, January 25, 2011 8:49 AM
To: NG HUI WEN; Gromacs Users' List
Subject: Re: [gmx-users] using Berger Lipids in gromacs 4.5.3


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:jalem...@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-boun...@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-boun...@gromacs.org
>>> [mailto:gmx-users-boun...@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  InputStructure 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 

Re: [gmx-users] using Berger Lipids in gromacs 4.5.3

[Justin A. Lemkul]

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:jalem...@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-boun...@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-boun...@gromacs.org
[mailto:gmx-users-boun...@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  InputStructure 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 -niceint0   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) -distreal
0.3 Maximum donor-acceptor distance for a H-bond (nm) -[no]una bool
no  Select aromatic rings with united CH atoms on Phenylalanine,
Tryptophan

Re: [gmx-users] using Berger Lipids in gromacs 4.5.3

[Justin A. Lemkul]

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-boun...@gromacs.org
[mailto:gmx-users-boun...@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  InputStructure 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 -niceint0   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) -distreal
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]ignhbool   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   1000Force constant for position
restraints -vsite   enum   noneConvert 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

RE: [gmx-users] using Berger Lipids in gromacs 4.5.3

[NG HUI WEN]

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.

Huiwen

-Original Message-
From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@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  InputStructure file: gro g96 pdb tpr
>etc.
>   -o prot_pdb2gmx.pdb  Output   Structure file: gro g96 pdb etc.
>   -pprot.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
> -niceint0   Set the nicelevel
> -chainsepenum   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)
> -distreal   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]ignhbool   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   1000Force constant for position restraints
> -vsite   enum   noneConvert atoms to virtual sites: none, hydrogens
> or aromatics
> -[no]heav

Re: [gmx-users] using Berger Lipids in gromacs 4.5.3

[Justin A. Lemkul]

 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: SPCsimple 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-boun...@gromacs.org [mailto:gmx-users-boun...@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-boun...@gromacs.org on behalf of NG HUI WEN
*Sent:* Sun 1/23/2011 1:40 PM
*To:* gmx-users@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@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 In

RE: [gmx-users] using Berger Lipids in gromacs 4.5.3

[NG HUI WEN]

k 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: SPCsimple 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?

Thanks a lot!

HW


-Original Message-
From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@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-boun...@gromacs.org on behalf of NG HUI WEN
> *Sent:* Sun 1/23/2011 1:40 PM
> *To:* gmx-users@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@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

Re: [gmx-users] using Berger Lipids in gromacs 4.5.3

[Justin A. Lemkul]

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-boun...@gromacs.org on behalf of NG HUI WEN
*Sent:* Sun 1/23/2011 1:40 PM
*To:* gmx-users@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@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  
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  InputStructure file: gro g96 pdb tpr etc.
  -o protein_pdb2gmx.pdb  Output   Structure file: gro g96 pdb etc.
  -pprotein.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
-niceint0   Set the nicelevel
-chainsepenum   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
   

RE: [gmx-users] using Berger Lipids in gromacs 4.5.3

[NG HUI WEN]

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-boun...@gromacs.org on behalf of NG HUI WEN
Sent: Sun 1/23/2011 1:40 PM
To: gmx-users@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@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   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  InputStructure file: gro g96 pdb tpr etc.
  -o protein_pdb2gmx.pdb  Output   Structure file: gro g96 pdb etc.
  -pprotein.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
-niceint0   Set the nicelevel
-chainsepenum   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)
-distreal   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]ignhbool   yes Ignore hydrogen atoms that are in the pdb file
-[no]missing bool   no