[gmx-users] Re: Lipid bilayer parameters (David)
Jim Kress
beowulf at kressworks.com
Sun Jul 24 22:19:46 CEST 2005
David,
Is this also bad:
Warning: atom names in topol.top and conf.gro don't match (OL1 - HW3)
Warning: atom names in topol.top and conf.gro don't match (OL2 - HW4)
Warning: atom names in topol.top and conf.gro don't match (OL1 - HW3)
Warning: atom names in topol.top and conf.gro don't match (OL2 - HW4)
Warning: atom names in topol.top and conf.gro don't match (OL1 - HW3)
Warning: atom names in topol.top and conf.gro don't match (OL2 - HW4)
Warning: atom names in topol.top and conf.gro don't match (OL1 - HW3)
Warning: atom names in topol.top and conf.gro don't match (OL2 - HW4)
Warning: atom names in topol.top and conf.gro don't match (OL1 - HW3)
Warning: atom names in topol.top and conf.gro don't match (OL2 - HW4)
Warning: atom names in topol.top and conf.gro don't match (OL1 - HW3)
Warning: atom names in topol.top and conf.gro don't match (OL2 - HW4)
Warning: atom names in topol.top and conf.gro don't match (OL1 - HW3)
Warning: atom names in topol.top and conf.gro don't match (OL2 - HW4)
Warning: atom names in topol.top and conf.gro don't match (OL1 - HW3)
Warning: atom names in topol.top and conf.gro don't match (OL2 - HW4)
Warning: atom names in topol.top and conf.gro don't match (OL1 - HW3)
Warning: atom names in topol.top and conf.gro don't match (OL2 - HW4)
Warning: atom names in topol.top and conf.gro don't match (OL1 - HW3)
Warning: atom names in topol.top and conf.gro don't match (OL2 - HW4)
(more than 20 non-matching atom names)
WARNING 1 [file "topol.top", line 423]:
21242 non-matching atom names
atom names from topol.top will be used
atom names from conf.gro will be ingnored
?? I'm doing TIP5P water. There is an inconsistency between the gromacs
supplied files, however. In ffoplsaa.rtp, TIP5P negative point charges are
called HW3 and HW4 while in tip5p.itp they are called OL1 and OL2,
respectively.
Is that the cause of the warning messages and can they be safely ignored?
Thanks.
Jim
> -----Original Message-----
> From: gmx-users-request at gromacs.org
> [mailto:gmx-users-request at gromacs.org]
> Sent: Sunday, July 24, 2005 6:00 AM
> To: gmx-users at gromacs.org
> Subject: gmx-users Digest, Vol 15, Issue 42
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> Today's Topics:
>
> 1. Lipid bilayer parameters (naga raju)
> 2. polymer NVT (javier sacristan)
> 3. Re: Lipid bilayer parameters (David)
> 4. Re: Lipid bilayer parameters (Tsjerk Wassenaar)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Sat, 23 Jul 2005 05:20:03 -0700 (PDT)
> From: naga raju <nagaraju_cy at yahoo.co.in>
> Subject: [gmx-users] Lipid bilayer parameters
> To: gmx-users at gromacs.org
> Message-ID: <20050723122003.81856.qmail at web8503.mail.in.yahoo.com>
> Content-Type: text/plain; charset=iso-8859-1
>
> Dear gmx-users,
> I built a lipid bilayer (72 lipid molecules
> and 2376 water molecules) by taking one lipid molecule from
> the dppc.pdb file in website:
> http://moose.bio.ucalgary.ca/index.php?page=Downloads
> I downloaded dppc.itp and lipid.itp files from the above
> link. when i used the grompp command, it shows the following error.
>
> Warning: atom names in dppc.top and bbww.pdb don't match (C1 - C2)
> Warning: atom names in dppc.top and bbww.pdb don't match (C2 - N4)
> Warning: atom names in dppc.top and bbww.pdb don't match (N4 - C5)
> Warning: atom names in dppc.top and bbww.pdb don't match (C5 - C6)
> Warning: atom names in dppc.top and bbww.pdb don't match (C6 - O7)
> Warning: atom names in dppc.top and bbww.pdb don't match (O7 - P8)
> Warning: atom names in dppc.top and bbww.pdb don't match (P8 - O9)
> Warning: atom names in dppc.top and bbww.pdb don't match (O9 - O10)
> Warning: atom names in dppc.top and bbww.pdb don't match (O10 - O11)
> Warning: atom names in dppc.top and bbww.pdb don't match (O11 - C12)
> Warning: atom names in dppc.top and bbww.pdb don't match (C12 - C13)
> Warning: atom names in dppc.top and bbww.pdb don't match (C13 - O14)
> Warning: atom names in dppc.top and bbww.pdb don't match (O14 - C15)
> Warning: atom names in dppc.top and bbww.pdb don't match (C15 - O16)
> Warning: atom names in dppc.top and bbww.pdb don't match (O16 - C17)
> Warning: atom names in dppc.top and bbww.pdb don't match (C17 - C18)
> Warning: atom names in dppc.top and bbww.pdb don't match (C18 - C19)
> Warning: atom names in dppc.top and bbww.pdb don't match (C19 - C20)
> Warning: atom names in dppc.top and bbww.pdb don't match (C20 - C21)
> Warning: atom names in dppc.top and bbww.pdb don't match (C21
> - C22) (more than 20 non-matching atom names) WARNING 1 [file
> "dppc.top", line 26]:
> 9096 non-matching atom names
> atom names from dppc.top will be used
> atom names from bbww.pdb will be ingnored
>
> double-checking input for internal consistency...
> ERROR: One of the box vectors is shorter than twice the
> cut-off length. Increase the box size or decrease rlist.
> There was 1 warning
>
>
> How can be the problem solved?
> Here i gave my dppc.top file:
>
> #include "ffgmx.itp"
> #include "lipid.itp"
> #include "dppc.itp"
> #include "alm.itp"
> #include "ions.itp"
>
> #ifdef FLEX_SPC
> #include "flexspc.itp"
> #else
> #include "spc.itp"
> #endif
>
> [ system ]
> ; name
> Alm on surf + relaxed popc
>
> [ molecules ]
> ; name number
> DPPC 72
> SOL 2376
>
>
> Thank you
> nagaraju
>
>
>
>
> ____________________________________________________
> Start your day with Yahoo! - make it your home page
> http://www.yahoo.com/r/hs
>
>
>
> ------------------------------
>
> Message: 2
> Date: Sat, 23 Jul 2005 07:39:52 -0600
> From: "javier sacristan" <jus29 at psu.edu>
> Subject: [gmx-users] polymer NVT
> To: <gmx-users at gromacs.org>
> Message-ID: <200507231339.j6NDdpR3102066 at f05n15.cac.psu.edu>
> Content-Type: text/plain; charset="US-ASCII"
>
> Thank you David I will try to do NPT with 100 bars and after
> with 1 bar.....
>
> I really appreciate your help.
>
> Last question I am doing the sim. with united atom model so,
> I think that
> i do not need to use constraints, it is just a linear
> polymer. (Gromacs
> 3.2.1)
>
> Thanks again
>
> Javier
>
>
> ------------------------------
>
> Message: 2
> Date: Sat, 23 Jul 2005 09:10:31 +0200 (CEST)
> From: David van der Spoel <spoel at xray.bmc.uu.se>
> Subject: Re: [gmx-users] polymer NVT
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID:
> <Pine.LNX.4.44.0507230908410.26987-100000 at rembrandt.bmc.uu.se>
> Content-Type: TEXT/PLAIN; charset=US-ASCII
>
> On Fri, 22 Jul 2005, javier wrote:
>
> >Dear Gromacssss
> >
> > My system consist of 1 polymer chain, and I need to do NVT
> simulations, so
> >I need to fix the box size according to my polymer density.
> > But I really do not understand editconf?
> >
> >My edit conf is: ediconf -bt cubic -f file.gro -o out.gro -d
> 0.5 -center
> >
> >But in this way I do not get the right density, so I have tried:
> >
> >
> >ediconf -bt cubic -f file.gro -o out.gro -d 0.5 -density 1010
> >
> >but the resulting box vector lengths are a=4 b=7 and c=0.3.
> Therefore I
> >only can use very small cutoffs due to the small c value.
> >
> >And my polymer chain does not look like a Gaussian chain,
> and it is outside
> >of the cell.
> >
> >So, do you have some idea?
>
> make a box of 7 7 7 that fits the chain
> do a simulation with pressure coupling to 100 bar and watch the box
> contract. then do sim with pressure 1 bar and check the final
> density. If
> it is not right check your force field.
>
> you need pbc = full for this kind of simulation (and
> constraint algorihtm
> LINCS with CVS code or no constraints with 3.2.1).
>
> >
> >.
> >
> >THANK YOU!!!!
> >
> >Javier
> >
> >_______________________________________________
> >gmx-users mailing list
> >gmx-users at gromacs.org
> >http://www.gromacs.org/mailman/listinfo/gmx-users
> >Please don't post (un)subscribe requests to the list. Use the
> >www interface or send it to gmx-users-request at gromacs.org.
> >
>
> --
> David.
> ______________________________________________________________
> __________
> David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
> Dept. of Cell and Molecular Biology, Uppsala University.
> Husargatan 3, Box 596, 75124 Uppsala, Sweden
> phone: 46 18 471 4205 fax: 46 18 511 755
> spoel at xray.bmc.uu.se spoel at gromacs.org http://xray.bmc.uu.se/~spoel
> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> ++++++++++
>
>
>
> ------------------------------
>
> _______________________________________________
> gmx-users mailing list
> gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
>
>
> End of gmx-users Digest, Vol 15, Issue 41
> *****************************************
>
>
>
>
> ------------------------------
>
> Message: 3
> Date: Sat, 23 Jul 2005 16:52:11 +0200
> From: David <spoel at xray.bmc.uu.se>
> Subject: Re: [gmx-users] Lipid bilayer parameters
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <1122130331.13585.0.camel at localhost.localdomain>
> Content-Type: text/plain
>
> On Sat, 2005-07-23 at 05:20 -0700, naga raju wrote:
> > Dear gmx-users,
> > I built a lipid bilayer (72 lipid
> > molecules and 2376 water molecules) by taking one
> > lipid molecule from the dppc.pdb file in website:
> > http://moose.bio.ucalgary.ca/index.php?page=Downloads
> > I downloaded dppc.itp and lipid.itp files from the
> > above link. when i used the grompp command, it shows
> > the following error.
> >
> > Warning: atom names in dppc.top and bbww.pdb don't
> > match (C1 - C2)
> this is bad.
> fix your top or pdb file such that they match.
>
> > Warning: atom names in dppc.top and bbww.pdb don't
> > match (C2 - N4)
> > Warning: atom names in dppc.top and bbww.pdb don't
> > match (N4 - C5)
> > Warning: atom names in dppc.top and bbww.pdb don't
> > match (C5 - C6)
> > Warning: atom names in dppc.top and bbww.pdb don't
> > match (C6 - O7)
> > Warning: atom names in dppc.top and bbww.pdb don't
> > match (O7 - P8)
> > Warning: atom names in dppc.top and bbww.pdb don't
> > match (P8 - O9)
> > Warning: atom names in dppc.top and bbww.pdb don't
> > match (O9 - O10)
> > Warning: atom names in dppc.top and bbww.pdb don't
> > match (O10 - O11)
> > Warning: atom names in dppc.top and bbww.pdb don't
> > match (O11 - C12)
> > Warning: atom names in dppc.top and bbww.pdb don't
> > match (C12 - C13)
> > Warning: atom names in dppc.top and bbww.pdb don't
> > match (C13 - O14)
> > Warning: atom names in dppc.top and bbww.pdb don't
> > match (O14 - C15)
> > Warning: atom names in dppc.top and bbww.pdb don't
> > match (C15 - O16)
> > Warning: atom names in dppc.top and bbww.pdb don't
> > match (O16 - C17)
> > Warning: atom names in dppc.top and bbww.pdb don't
> > match (C17 - C18)
> > Warning: atom names in dppc.top and bbww.pdb don't
> > match (C18 - C19)
> > Warning: atom names in dppc.top and bbww.pdb don't
> > match (C19 - C20)
> > Warning: atom names in dppc.top and bbww.pdb don't
> > match (C20 - C21)
> > Warning: atom names in dppc.top and bbww.pdb don't
> > match (C21 - C22)
> > (more than 20 non-matching atom names)
> > WARNING 1 [file "dppc.top", line 26]:
> > 9096 non-matching atom names
> > atom names from dppc.top will be used
> > atom names from bbww.pdb will be ingnored
> >
> > double-checking input for internal consistency...
> > ERROR: One of the box vectors is shorter than twice
> > the cut-off length. Increase the box size or decrease
> > rlist.
> > There was 1 warning
> >
> >
> > How can be the problem solved?
> > Here i gave my dppc.top file:
> >
> > #include "ffgmx.itp"
> > #include "lipid.itp"
> > #include "dppc.itp"
> > #include "alm.itp"
> > #include "ions.itp"
> >
> > #ifdef FLEX_SPC
> > #include "flexspc.itp"
> > #else
> > #include "spc.itp"
> > #endif
> >
> > [ system ]
> > ; name
> > Alm on surf + relaxed popc
> >
> > [ molecules ]
> > ; name number
> > DPPC 72
> > SOL 2376
> >
> >
> > Thank you
> > nagaraju
> >
> >
> >
> >
> > ____________________________________________________
> > Start your day with Yahoo! - make it your home page
> > http://www.yahoo.com/r/hs
> >
> > _______________________________________________
> > gmx-users mailing list
> > gmx-users at gromacs.org
> > http://www.gromacs.org/mailman/listinfo/gmx-users
> > Please don't post (un)subscribe requests to the list. Use the
> > www interface or send it to gmx-users-request at gromacs.org.
> --
> David.
> ______________________________________________________________
> __________
> David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
> Dept. of Cell and Molecular Biology, Uppsala University.
> Husargatan 3, Box 596, 75124 Uppsala, Sweden
> phone: 46 18 471 4205 fax: 46 18 511 755
> spoel at xray.bmc.uu.se spoel at gromacs.org
> http://xray.bmc.uu.se/~spoel
> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> ++++++++++
>
>
>
> ------------------------------
>
> Message: 4
> Date: Sun, 24 Jul 2005 10:21:04 +0200
> From: Tsjerk Wassenaar <tsjerkw at gmail.com>
> Subject: Re: [gmx-users] Lipid bilayer parameters
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <8ff898150507240121385b3383 at mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
>
> Hi Nagaraju,
>
> It looks like you miss the first atom in the pdb file (which should be
> a C1). In addition, check your box, since there's something wrong with
> that too, according to the grompp output.
>
> Hope it helps,
>
> Tsjerk
>
> On 7/23/05, David <spoel at xray.bmc.uu.se> wrote:
> > On Sat, 2005-07-23 at 05:20 -0700, naga raju wrote:
> > > Dear gmx-users,
> > > I built a lipid bilayer (72 lipid
> > > molecules and 2376 water molecules) by taking one
> > > lipid molecule from the dppc.pdb file in website:
> > > http://moose.bio.ucalgary.ca/index.php?page=Downloads
> > > I downloaded dppc.itp and lipid.itp files from the
> > > above link. when i used the grompp command, it shows
> > > the following error.
> > >
> > > Warning: atom names in dppc.top and bbww.pdb don't
> > > match (C1 - C2)
> > this is bad.
> > fix your top or pdb file such that they match.
> >
> > > Warning: atom names in dppc.top and bbww.pdb don't
> > > match (C2 - N4)
> > > Warning: atom names in dppc.top and bbww.pdb don't
> > > match (N4 - C5)
> > > Warning: atom names in dppc.top and bbww.pdb don't
> > > match (C5 - C6)
> > > Warning: atom names in dppc.top and bbww.pdb don't
> > > match (C6 - O7)
> > > Warning: atom names in dppc.top and bbww.pdb don't
> > > match (O7 - P8)
> > > Warning: atom names in dppc.top and bbww.pdb don't
> > > match (P8 - O9)
> > > Warning: atom names in dppc.top and bbww.pdb don't
> > > match (O9 - O10)
> > > Warning: atom names in dppc.top and bbww.pdb don't
> > > match (O10 - O11)
> > > Warning: atom names in dppc.top and bbww.pdb don't
> > > match (O11 - C12)
> > > Warning: atom names in dppc.top and bbww.pdb don't
> > > match (C12 - C13)
> > > Warning: atom names in dppc.top and bbww.pdb don't
> > > match (C13 - O14)
> > > Warning: atom names in dppc.top and bbww.pdb don't
> > > match (O14 - C15)
> > > Warning: atom names in dppc.top and bbww.pdb don't
> > > match (C15 - O16)
> > > Warning: atom names in dppc.top and bbww.pdb don't
> > > match (O16 - C17)
> > > Warning: atom names in dppc.top and bbww.pdb don't
> > > match (C17 - C18)
> > > Warning: atom names in dppc.top and bbww.pdb don't
> > > match (C18 - C19)
> > > Warning: atom names in dppc.top and bbww.pdb don't
> > > match (C19 - C20)
> > > Warning: atom names in dppc.top and bbww.pdb don't
> > > match (C20 - C21)
> > > Warning: atom names in dppc.top and bbww.pdb don't
> > > match (C21 - C22)
> > > (more than 20 non-matching atom names)
> > > WARNING 1 [file "dppc.top", line 26]:
> > > 9096 non-matching atom names
> > > atom names from dppc.top will be used
> > > atom names from bbww.pdb will be ingnored
> > >
> > > double-checking input for internal consistency...
> > > ERROR: One of the box vectors is shorter than twice
> > > the cut-off length. Increase the box size or decrease
> > > rlist.
> > > There was 1 warning
> > >
> > >
> > > How can be the problem solved?
> > > Here i gave my dppc.top file:
> > >
> > > #include "ffgmx.itp"
> > > #include "lipid.itp"
> > > #include "dppc.itp"
> > > #include "alm.itp"
> > > #include "ions.itp"
> > >
> > > #ifdef FLEX_SPC
> > > #include "flexspc.itp"
> > > #else
> > > #include "spc.itp"
> > > #endif
> > >
> > > [ system ]
> > > ; name
> > > Alm on surf + relaxed popc
> > >
> > > [ molecules ]
> > > ; name number
> > > DPPC 72
> > > SOL 2376
> > >
> > >
> > > Thank you
> > > nagaraju
> > >
> > >
> > >
> > >
> > > ____________________________________________________
> > > Start your day with Yahoo! - make it your home page
> > > http://www.yahoo.com/r/hs
> > >
> > > _______________________________________________
> > > gmx-users mailing list
> > > gmx-users at gromacs.org
> > > http://www.gromacs.org/mailman/listinfo/gmx-users
> > > Please don't post (un)subscribe requests to the list. Use the
> > > www interface or send it to gmx-users-request at gromacs.org.
> > --
> > David.
> >
> ______________________________________________________________
> __________
> > David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
> > Dept. of Cell and Molecular Biology, Uppsala University.
> > Husargatan 3, Box 596, 75124 Uppsala, Sweden
> > phone: 46 18 471 4205 fax: 46 18 511 755
> > spoel at xray.bmc.uu.se spoel at gromacs.org
> http://xray.bmc.uu.se/~spoel
> >
> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> ++++++++++
> >
> > _______________________________________________
> > gmx-users mailing list
> > gmx-users at gromacs.org
> > http://www.gromacs.org/mailman/listinfo/gmx-users
> > Please don't post (un)subscribe requests to the list. Use the
> > www interface or send it to gmx-users-request at gromacs.org.
> >
>
>
> ------------------------------
>
> _______________________________________________
> gmx-users mailing list
> gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
>
>
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