[gmx-users] No default Proper Dih. types, using zeroes

anwar at cdfd.org.in anwar at cdfd.org.in
Fri Jul 29 06:17:52 CEST 2005


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?
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
>> >
>> >
>>
>> _______________________________________________
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> --
> 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 --------------
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> ------------------------------
>
> 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
---------------------------------------------




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