[gmx-users] Re: Lipid bilayer parameters (David)
David
spoel at xray.bmc.uu.se
Mon Jul 25 08:47:29 CEST 2005
On Sun, 2005-07-24 at 16:19 -0400, Jim Kress wrote:
> 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?
This is not a problem. After a short run and/or minimization they will
be named properly.
>
> 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
> >
> >
> > End of gmx-users Digest, Vol 15, Issue 42
> > *****************************************
> >
> >
> >
>
> _______________________________________________
> 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
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