[gmx-users] No default Proper Dih. types, using zeroes
David
spoel at xray.bmc.uu.se
Fri Jul 29 09:35:01 CEST 2005
On Fri, 2005-07-29 at 12:17 +0800, anwar at cdfd.org.in wrote:
> Dear users,
> I am working on DNA simulations and I have encountered a problem while
> running grompp. It generates warnings and finally stops.
> "No default Proper Dih. types, using zeroes"
> What I think is that the dihedrals for that atoms is not defined in the
> database. If I have to do so then how do I do it? I can define a new
> dihedral angle, but how can I calculate the other parameters to include
> in the database. I mean to say is there any software to whihc detect
> all these parameters?
depends on force field, some have recipes how to determine new
parameters using e.g. quantum calculations.
> regards
> Anwar
>
>
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> > Today's Topics:
> >
> > 1. Insertion of protein in lipid bilayer (John Simms)
> > 2. Re: 3.3beta vs 3.2 dispersion correction term (Sukit Leekumjorn)
> > 3. Re: 3.3beta vs 3.2 dispersion correction term (David)
> > 4. RE: Insertion of protein in lipid bilayer (rob yang)
> > 5. Need Help (Ur-Rehman, Saif )
> > 6. calculate the orientation of a group (David Haubertin)
> > 7. Re: calculate the orientation of a group (David)
> >
> >
> > ----------------------------------------------------------------------
> >
> > Message: 1
> > Date: Thu, 28 Jul 2005 11:34:46 +0100
> > From: "John Simms" <JXS818 at bham.ac.uk>
> > Subject: [gmx-users] Insertion of protein in lipid bilayer
> > To: <gmx-users at gromacs.org>
> > Message-ID:
> > <FDA2FCB72CDB2D408EE9CC6B766F6AF70A6970 at bioex1.adf.bham.ac.uk>
> > Content-Type: text/plain; charset="utf-8"
> >
> > Hi nagaraju,
> > What you need to do is to change the DPPC to DPP in the command line,
> > perl make_hole.pl -f dppc.pdb -o outbilayer.pdb -r 1.4 -lipat P8 -lipid
> > DPPC -cx 3.2 -cy 3.2
> > as this is what is defined in the PDB file. After you have done this you
> > will need to change the number of DPP molecules in the .top file. Also
> > make such that you renumber the last water atoms to be consistent with the
> > input file AFTER the initial hole has been made.
> > Cheers
> > John
> >
> >
> > ------------------------------
> >
> > Message: 2
> > Date: Thu, 28 Jul 2005 10:38:02 -0400
> > From: Sukit Leekumjorn <leekumjo at vt.edu>
> > Subject: Re: [gmx-users] 3.3beta vs 3.2 dispersion correction term
> > To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> > Message-ID: <42E8EDCA.9080704 at vt.edu>
> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed
> >
> > Thank your for your reply, David
> >
> > I downloaded the beta version on July 8 2005 from the CVS usage
> > website. I noticed that the heading of the program is in VERSION
> > 3.3_beta_20050202. I am not certain if this is the latest version. If it
> > is not, can you please let me know the patches for the latest version.
> >
> > Sukit
> >
> > David wrote:
> >
> >>On Wed, 2005-07-27 at 16:58 -0400, Sukit Leekumjorn wrote:
> >>
> >>
> >>>Thank you for your reply, David
> >>>
> >>>Sorry about not comparing things one at a time. I took your suggestion
> >>>and tried comparing both cutoff (rvdw=1 and rcoulomb=1.8) and pme
> >>>(rvdw=0.9 and rcoulomb=0.9) for both versions without corrections; and
> >>>it turns out to be almost exactly the same. I then took an additional
> >>>step to compare the pme simulation including the correction factor for
> >>>both versions. Listed below is the total energy caculated in step 0.
> >>>You mentioned that the corrction factor in 3.2.1 version is not correct
> >>>and it is fixed in the 3.3B version, I am not sure if this is normal for
> >>>the correction factor to be 2 orders of magnitude higher, which greatly
> >>>effects the total energy of the system.
> >>>
> >>>3.2.1 cutoff: -1.71612e+6
> >>>3.2.1 pme without correction: -1.69195e+6
> >>>3.2.1 pme with correction: -1.69664e+6 (Disp Corr = -4.69360e+3)
> >>>
> >>>3.3B cutoff: -1.71385e+6
> >>>3.3B pme without correction: -1.69413e+6
> >>>3.3B pme with correction: -1.96249e+6 (Disp Corr = -2.68357e+5)
> >>>
> >>>
> >>I get different numbers (step 0 only):
> >>PME with correction Total energy -1.73585e+06 (Disp corr -3.54849e+04)
> >>
> >>Are you sure you have the latest version? There have been changes in
> >>this code in april, see:
> >>http://www.gromacs.org/features/changes33.html
> >>
> >>
> >
> >
> >
> > ------------------------------
> >
> > Message: 3
> > Date: Thu, 28 Jul 2005 17:00:46 +0200
> > From: David <spoel at xray.bmc.uu.se>
> > Subject: Re: [gmx-users] 3.3beta vs 3.2 dispersion correction term
> > To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> > Message-ID: <1122562846.19088.0.camel at localhost.localdomain>
> > Content-Type: text/plain
> >
> > On Thu, 2005-07-28 at 10:38 -0400, Sukit Leekumjorn wrote:
> >> Thank your for your reply, David
> >>
> >> I downloaded the beta version on July 8 2005 from the CVS usage
> >> website. I noticed that the heading of the program is in VERSION
> >> 3.3_beta_20050202. I am not certain if this is the latest version. If it
> >> is not, can you please let me know the patches for the latest version.
> >>
> > if you used CVS then you can get later patches by typing
> > cvs update
> > I'm afraid that doesn't explain it however.
> >
> >> Sukit
> >>
> >> David wrote:
> >>
> >> >On Wed, 2005-07-27 at 16:58 -0400, Sukit Leekumjorn wrote:
> >> >
> >> >
> >> >>Thank you for your reply, David
> >> >>
> >> >>Sorry about not comparing things one at a time. I took your
> >> suggestion
> >> >>and tried comparing both cutoff (rvdw=1 and rcoulomb=1.8) and pme
> >> >>(rvdw=0.9 and rcoulomb=0.9) for both versions without corrections; and
> >> >>it turns out to be almost exactly the same. I then took an additional
> >> >>step to compare the pme simulation including the correction factor for
> >> >>both versions. Listed below is the total energy caculated in step 0.
> >> >>You mentioned that the corrction factor in 3.2.1 version is not
> >> correct
> >> >>and it is fixed in the 3.3B version, I am not sure if this is normal
> >> for
> >> >>the correction factor to be 2 orders of magnitude higher, which
> >> greatly
> >> >>effects the total energy of the system.
> >> >>
> >> >>3.2.1 cutoff: -1.71612e+6
> >> >>3.2.1 pme without correction: -1.69195e+6
> >> >>3.2.1 pme with correction: -1.69664e+6 (Disp Corr = -4.69360e+3)
> >> >>
> >> >>3.3B cutoff: -1.71385e+6
> >> >>3.3B pme without correction: -1.69413e+6
> >> >>3.3B pme with correction: -1.96249e+6 (Disp Corr = -2.68357e+5)
> >> >>
> >> >>
> >> >I get different numbers (step 0 only):
> >> >PME with correction Total energy -1.73585e+06 (Disp corr
> >> -3.54849e+04)
> >> >
> >> >Are you sure you have the latest version? There have been changes in
> >> >this code in april, see:
> >> >http://www.gromacs.org/features/changes33.html
> >> >
> >> >
> >>
> >> _______________________________________________
> >> 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: Thu, 28 Jul 2005 10:44:30 -0500
> > From: "rob yang" <nextgame at hotmail.com>
> > Subject: RE: [gmx-users] Insertion of protein in lipid bilayer
> > To: gmx-users at gromacs.org
> > Message-ID: <BAY104-F11C7F3D2C1157081BD321C6CF0 at phx.gbl>
> > Content-Type: text/plain; format=flowed
> >
> > Hello gmx'ers,
> > I've been struggling with setting up md simulations of glycophorin A in
> > POPC
> > environment. I downloaded the make_hole program by Graham Smith and
> > followed
> > the tutorial as best as I could. My 2 layers of membranes fell apart (from
> > looking at the trp file) and after about 130ps I got the following error:
> >
> > -----
> > Grid: 17 x 16 x 19 cells
> > WARNING: your box is exploding! (ncells = 5168)
> > atomic surface: building atom-vertex nn list...
> > ----
> >
> > So obviously there's some kinda user errors here as I used arbitrary
> > parameters and what not. This is my input files:
> > ----
> > topology file:
> > #include "ffgmx.itp"
> > #include "popc.itp"
> > #ifdef FLEX_SPC
> > #include "flexspc.itp"
> > #else
> > #include "spc.itp"
> > #endif
> > [ molecules ]
> > ; name number
> > POPC 39
> > SOL 770
> > ----
> > lipid.mdp file:
> > define = -DPOSRES
> > integrator = md
> > dt = 0.002
> > nsteps = 500000
> > nstxout = 5000
> > nstvout = 5000
> > nstlog = 5000
> > nstenergy = 250
> > nstxtcout = 250
> > xtc_grps = POPC SOL
> > energygrps = POPC SOL
> > nstlist = 10
> > ns_type = grid
> > rlist = 0.9
> > coulombtype = PME
> > rcoulomb = 0.9
> > rvdw = 0.9
> > vdw-type = Cut-off
> > tcoupl = Berendsen
> > tc-grps = POPC SOL
> > tau_t = 0.1 0.1
> > ref_t = 300 300
> > Pcoupl = Berendsen
> > tau_p = 20
> > compressibility = 4.5e-5
> > ref_p = 1.0
> > gen_vel = yes
> > gen_temp = 300
> > gen_seed = 173529
> > ;solvent_optimization = SOL
> > constraints = all-bonds
> > ---
> > hp.mdp file:
> > holetype = MSMS
> > hfm = 10
> > supf = 20
> > molsurf_log = gsurf.log
> > hz = -2.61
> > hp1 = 1
> > hp2 = 2028
> > s1 = 2029
> > s2 = 4338
> > hz1 = -26.28
> > hz2 = 26.43
> > sfm = 10.0
> > sofs = 0.15
> > molsurf_file = ./gpa1_msms
> > debugsurf = no
> > resforces = yes
> >
> > I don't want to re-invent the wheels here since I am only trying to learn
> > the protocol so that I can apply it to other membrane proteins later. So
> > if
> > anybody has done simulations using the make_hole program and wouldn't mind
> > posting sample parameter files (.top, .mdp, etc) or sample system with
> > results (bible for us newbies), I would really appreciate it.
> >
> > Thank you very much in advance.
> >
> > Rob
> >
> >
> >
> >
> > ------------------------------
> >
> > Message: 5
> > Date: Thu, 28 Jul 2005 16:38:12 +0100
> > From: "Ur-Rehman, Saif " <su7 at hw.ac.uk>
> > Subject: [gmx-users] Need Help
> > To: <gmx-users at gromacs.org>
> > Message-ID:
> > <B5B4FC1CC0024646A381EE5236AFF6CA24C4C1 at ex1.mail.win.hw.ac.uk>
> > Content-Type: text/plain; charset="iso-8859-1"
> >
> > I am trying to run a simulated annaeling simulation on a 6 residue peptide
> > which i chopped out of beta lactoglobulin.
> > I am using Windows and grommpp absolutely refuses to work. I have read a
> > previous posting that this error is down to the path for the cpp not being
> > set right in the mdp file. However no matter how i change the path it
> > results in this error
> > I think it might have to do with the fact that theres a space in the path.
> > however i cannot reinstall it as i do not have the privileges on the
> > network to do so. Is there a way round this kind of situation
> >
> > Thanking you in advance
> >
> > Saif
> >
> > grompp.mdp has this in it at the moment
> > title = Beta-Lac
> >
> > cpp = c:\Progra~1\Gromacs\bin\cpp
> >
> > include = -I C:\Progra~1\Gromacs\share\top
> >
> >
> > and running grompp results in
> >
> > calling c:\Progra~1\Gromacs\bin\cpp...
> > \Progra~1\Gromacs\bin\cpp: Files\Gromacs\share\top: No such file or
> > directory
> > cpp exit code: 33
> > Tried to execute: 'c:\Progra~1\Gromacs\bin\cpp -I
> > C:\Progra~1\Gromacs\share\top
> > -I D:\Gromacs\share\top -IC:\Program Files\Gromacs\share\top topol.top >
> > grompp
> > a01720'
> > The 'c:\Progra~1\Gromacs\bin\cpp' command is defined in the .mdp file
> > processing topology...
> > processing coordinates...
> > Fatal error: number of coordinates in coordinate file (conf.gro, 23727)
> > does not match topology (topol.top, 0)
> > -------------- next part --------------
> > An HTML attachment was scrubbed...
> > URL:
> > http://www.gromacs.org/pipermail/gmx-users/attachments/20050728/ffde0848/attachment-0001.htm
> >
> > ------------------------------
> >
> > Message: 6
> > Date: 28 Jul 2005 16:58:55 +0200
> > From: David Haubertin <david.haubertin at cea.fr>
> > Subject: [gmx-users] calculate the orientation of a group
> > To: gmx-users at gromacs.org
> > Message-ID: <1122562734.2032.11.camel at yotam>
> > Content-Type: text/plain; charset=UTF-8
> >
> > Hi all,
> >
> > I would like to calculate the orientation of a group in my simulation
> > and cant figure out how to do it.
> >
> > I have a protein in a membrane, a large part of this protein is in the
> > solvent and has a rigid-body like motion. I'd like to characterise that
> > motion by let's say monitoring the evolution of the principal axis of
> > inertia.
> >
> > I thought about g_gyrate, but could only retrieve moments of inertia,
> > not the proper axis.
> >
> > I then thought about g_dipole, but it crashes when I ask for a subgroup.
> >
> > Any thoughts on that?
> >
> > Thanks in advance
> >
> > David
> >
> >
> > --
> >
> > David HAUBERTIN Tel : (+33) 1 69 08 28 63
> > Commissariat à l'Energie Atomique - Centre de Saclay
> > Bat. 528 - DSV/DBJC/SBFM - 91191 Gif-sur-Yvette Cedex
> > email : dyh at cea.fr
> >
> >
> >
> >
> > ------------------------------
> >
> > Message: 7
> > Date: Thu, 28 Jul 2005 21:01:40 +0200
> > From: David <spoel at xray.bmc.uu.se>
> > Subject: Re: [gmx-users] calculate the orientation of a group
> > To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> > Message-ID: <1122577300.4641.6.camel at localhost.localdomain>
> > Content-Type: text/plain
> >
> > On Thu, 2005-07-28 at 16:58 +0200, David Haubertin wrote:
> >> Hi all,
> >>
> >> I would like to calculate the orientation of a group in my simulation
> >> and cant figure out how to do it.
> >>
> >> I have a protein in a membrane, a large part of this protein is in the
> >> solvent and has a rigid-body like motion. I'd like to characterise that
> >> motion by let's say monitoring the evolution of the principal axis of
> >> inertia.
> >>
> >> I thought about g_gyrate, but could only retrieve moments of inertia,
> >> not the proper axis.
> > You can rotate the whole box along the principal moments (using
> > editconf) and the rotation matrix should give you the answer. I don't
> > think it's printed though
> >>
> >> I then thought about g_dipole, but it crashes when I ask for a subgroup.
> >>
> >> Any thoughts on that?
> > How about g_bundle ?
> >
> >
> >>
> >> Thanks in advance
> >>
> >> David
> >>
> >>
> > --
> > 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 54
> > *****************************************
> >
>
>
> ---------------------------------------------
> Mohd Anwaruddin
> Project Assistant
> Lab of Computational Biology
> Center for DNA Fingerprinting and Diagnostics
> Nacharam,
> Hyderabad
> India
> ---------------------------------------------
>
> _______________________________________________
> 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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