[gmx-users] pdb2gmx and terminal proline
Graham E Jackson
jackson at science.uct.ac.za
Wed Nov 26 08:22:00 CET 2003
Dear All,
I have used pdb2gmx to convert a pdb file of a cyclic SS peptide built
in INSIGHT. The peptide has an N-terminal proline. The command line I
used was:
pdb2gmx -f mol.pdb -o mol.gro -p mol.top -ss -ter -ignh
Forcefield: 0 or 2 or 5
Link Cys Cys: y
N-term option: 1 (PRO-NH)
C-term option: 2 (none)
If I look at the structure generated with gOpenMol or vmd the NH of
proline is linked to C6 with a very unusual bridging H. If I look at
the topology file the H is only bonded to the proline N. However if I
view the structure with ngmx the H is not bridging but the bond angles
are all wrong for an sp3 N and the H is near C6.
Any help?
Graham.
gmx-users-request at gromacs.org wrote:
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> Today's Topics:
>
> 1. down with MPI (=?ISO-8859-1?B?Sm/jbyBDYXJsb3MgQw==?=amera Junior)
> 2. Re: down with MPI (David van der Spoel)
> 3. g_rdf (parinald at unsl.edu.ar)
> 4. quick fix for g_covar? (barrett)
> 5. multiple simulations (Nguyen Hoang Phuong)
> 6. Re: multiple simulations (David van der Spoel)
> 7. Re: CVS version (gilles)
> 8. Re: quick fix for g_covar? (Berk Hess)
> 9. Re: Re: quick fix for g_covar? (Ruben Martinez Buey)
> 10. Re: quick fix for g_covar? (Berk Hess)
> 11. Re: Imaging Problem (Ilya Chorny)
> 12. Re: replica exchange (Luca Monticelli)
> 13. Re: replica exchange (Ilya Chorny)
> 14. Re: g_rdf (Dallas Warren)
> 15. Problem on processing proteins consisting of two chains (wang chuanming)
>
> --__--__--
>
> Message: 1
> Date: Tue, 25 Nov 2003 10:17:19 -0200
> From: =?ISO-8859-1?B?Sm/jbyBDYXJsb3MgQw==?=amera Junior <camera at df.ibilce.unesp.br>
> To: gmx-users at gromacs.org
> Subject: [gmx-users] down with MPI
> Reply-To: gmx-users at gromacs.org
>
> Hi,
>
> When i running my mdrun in a beowulf cluster with 16 nodes, the network
> down in a few hours. What can be wrong?
>
> thanks in advanced,
>
> -------------------------------------------------
> This mail sent through IMP: http://horde.org/imp/
>
> --__--__--
>
> Message: 2
> Subject: Re: [gmx-users] down with MPI
> From: David van der Spoel <spoel at xray.bmc.uu.se>
> To: gmx-users at gromacs.org
> Organization:
> Date: 25 Nov 2003 13:35:28 +0100
> Reply-To: gmx-users at gromacs.org
>
> On Tue, 2003-11-25 at 13:17, =?ISO-8859-1?B?Sm/jbyBDYXJsb3MgQw==?=amera
> Junior wrote:
> > Hi,
> >
> > When i running my mdrun in a beowulf cluster with 16 nodes, the network
> > down in a few hours. What can be wrong?
> >
> anything.
> be more specific, but you may have to ask somewhere else.
> >
> > thanks in advanced,
> >
> >
> > -------------------------------------------------
> > This mail sent through IMP: http://horde.org/imp/
> > _______________________________________________
> > gmx-users mailing list
> > gmx-users at gromacs.org
> > http://www.gromacs.org/mailman/listinfo/gmx-users
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> > www interface or send it to gmx-users-request at gromacs.org.
> --
> David.
> ________________________________________________________________________
> David van der Spoel, PhD, Assist. 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: 3
> Date: Tue, 25 Nov 2003 10:07:11 -0300 (ART)
> From: <parinald at unsl.edu.ar>
> To: gmx-users at gromacs.org
> Subject: [gmx-users] g_rdf
> Reply-To: gmx-users at gromacs.org
>
> Hello gmx`ers:
> I have Cl- and Na+ en water, how I can do the rdf
> to: Oxigen with Cl-, Oxigen with Na+, Hidrogen with Na+, Hidrogen
> with CL-?
> Thank you. Pablo.
>
> --__--__--
>
> Message: 4
> From: "barrett" <barrett at biop.ox.ac.uk>
> To: <gmx-users at gromacs.org>
> Date: Tue, 25 Nov 2003 13:24:58 -0000
> Subject: [gmx-users] quick fix for g_covar?
> Reply-To: gmx-users at gromacs.org
>
> The fix to write_xpm3 described in the attached link would be very
> useful to me.
>
> http://www.gromacs.org/pipermail/gmx-developers/2003-July/000539.html
>
> We have an existing 3.1.4 build which I don't really want to recompile
> from scratch. The only use I really have for this at the moment is the
> g_covar command to get xpm files. Is there an easy way of getting an
> updated g_covar by itself?
>
> (running on PC cluster running Redhat linux)
>
> many thanks
>
> Paul
>
> Dr Paul Barrett
> Laboratory of Molecular Biophysics
> Department of Biochemistry
> University of Oxford
> Oxford
> OX1 3QU
>
> Tel 01865 275380
> Fax 01865 275182
>
> barrett at biop.ox.ac.uk
> hellopaul1 at hotmail.com
>
> --__--__--
>
> Message: 5
> Date: Tue, 25 Nov 2003 14:25:55 +0100 (MET)
> From: Nguyen Hoang Phuong <phuong at theochem.uni-frankfurt.de>
> To: gmx-users at gromacs.org
> Subject: [gmx-users] multiple simulations
> Reply-To: gmx-users at gromacs.org
>
> Dear All,
>
> what is the meaning of the option -multi in mdrun program?
>
> I thought that with this option, multiple simluations will run in
> parallel. However, I get only one simulation is run. I did as the following
>
> grompp -f md1.mdp -c md1.gro -p x.top -o md1.tpr -np 1
> grompp -f md2.mdp -c md2.gro -p x.top -o md2.tpr -np 1
>
> mdrun -multi -np 2 -s md1.tpr md2.tpr
>
> but only the simulation with md1.tpr is run.
>
> What the problem is?
>
> Phuong
>
> --__--__--
>
> Message: 6
> Subject: Re: [gmx-users] multiple simulations
> From: David van der Spoel <spoel at xray.bmc.uu.se>
> To: gmx-users at gromacs.org
> Organization:
> Date: 25 Nov 2003 14:33:48 +0100
> Reply-To: gmx-users at gromacs.org
>
> On Tue, 2003-11-25 at 14:25, Nguyen Hoang Phuong wrote:
> > Dear All,
> >
> > what is the meaning of the option -multi in mdrun program?
> >
> > I thought that with this option, multiple simluations will run in
> > parallel. However, I get only one simulation is run. I did as the following
> >
> > grompp -f md1.mdp -c md1.gro -p x.top -o md1.tpr -np 1
> > grompp -f md2.mdp -c md2.gro -p x.top -o md2.tpr -np 1
> >
> > mdrun -multi -np 2 -s md1.tpr md2.tpr
> >
> > but only the simulation with md1.tpr is run.
> >
> > What the problem is?
> you still need to run with mpirun
>
> >
> > Phuong
> >
> > _______________________________________________
> > 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, Assist. 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: 7
> Date: Tue, 25 Nov 2003 15:54:00 +0100 (CET)
> From: gilles <gilles at chem.rug.nl>
> To: <gmx-users at gromacs.org>
> Subject: Re: [gmx-users] CVS version
> Reply-To: gmx-users at gromacs.org
>
> Hi Alan,
>
> automake 1.7.x does not work with the current cvs snapshot, you have to
> use automake 1.5.x instead to create your Makefile.
>
> Gilles
>
> On Fri, 31 Oct 2003, Alan Wilter Sousa da Silva wrote:
>
> > Hi List!
> > I need help to compiled cvs version.
> > I never had problem before. But now I'm having problems. I also took a
> > look at Mailing-List archives, but I didn't get much.
> >
> > I'm using Mandrake 9.1 and had to install autoconf2.5-2.57-3mdk
> > e automake1.6-1.7.2-3mdk.
> >
> > automake (GNU automake) 1.7.2
> >
> > autoconf (GNU Autoconf) 2.57
> >
> > Now running ./bootstrap I got:
> >
> > -----------------------------------------------
> > ./bootstrap
> > share/template/Makefile.am:16: CFLAGS was already defined in condition
> > TRUE, which implies condition DOUBLE_TRUE ...
> > configure.ac:211: ... `CFLAGS' previously defined here.
> > share/template/Makefile.am:18: CFLAGS was already defined in condition
> > TRUE, which implies condition DOUBLE_FALSE ...
> > src/tools/Makefile.am: object `lsq.$(OBJEXT)' created both with libtool
> > and without
> > src/tools/Makefile.am: object `dlist.$(OBJEXT)' created both with libtool
> > and without
> > ------------------------------------------------
> > Anyway, a configure file is generated.
> >
> > Now running ./configure:
> >
> > ------------------------------------------------
> > ./configure
> > [... ok]
> > checking if the C compiler supports inline assembly... yes
> > configure: error: conditional "am__fastdepCXX" was never defined.
> > Usually this means the macro was only invoked conditionally.
> > ------------------------------------------------
> >
> > So I got no Makefile!
> >
> > Any help here, please!
> >
> > Cheers,
> >
> > --------------------------
> > Alan Wilter Sousa da Silva
> > --------------------------
> > B.Sc. - Dep. Física - UFPA
> > M.Sc. - Dep. Física - PUC/RJ
> > D.Sc. - IBCCF/UFRJ
> > Bolsista Pesquisador LAC-INPE
> > São José dos Campos (SP), Brasil
> > www.lac.inpe.br/~alan
> > _______________________________________________
> > 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.
> >
>
> --
>
> ------------------------------------------------------------------------
> | Hi! I'm a .signature virus! |
> | Copy me into your ~/.signature to help me spread! |
> ------------------------------------------------------------------------
> |Gilles Pieffet |
> |Molecular Dynamics Group |
> |Dept. of Biophysical Chemistry |
> |University of Groningen |
> |Nijenborgh 4 |
> |9747 AG Groningen |
> |The Netherlands |
> |_______________________________________________|
>
> --__--__--
>
> Message: 8
> From: "Berk Hess" <gmx3 at hotmail.com>
> To: gmx-users at gromacs.org
> Subject: [gmx-users] Re: quick fix for g_covar?
> Date: Tue, 25 Nov 2003 15:58:15 +0100
> Reply-To: gmx-users at gromacs.org
>
> >Is there an easy way of getting an updated g_covar by itself?
> >
> >(running on PC cluster running Redhat linux)
> >
> >many thanks
> >
> >Paul
>
> I sent you a binary by email.
> This new g_covar of the soon to be release 3.2.0 version also calculates
> the covariance matrix in a more accurate way.
>
> Berk.
>
> _________________________________________________________________
> Protect your PC - get McAfee.com VirusScan Online
> http://clinic.mcafee.com/clinic/ibuy/campaign.asp?cid=3963
>
> --__--__--
>
> Message: 9
> Date: Tue, 25 Nov 2003 16:38:13 +0100
> From: Ruben Martinez Buey <ruben at akilonia.cib.csic.es>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Re: quick fix for g_covar?
> Reply-To: gmx-users at gromacs.org
>
> Hi Berk,
> Where can I get this new g_covar?
> Thanks in advance
> best wishes,
> Ruben
>
> Berk Hess wrote:
>
> >> Is there an easy way of getting an updated g_covar by itself?
> >>
> >> (running on PC cluster running Redhat linux)
> >>
> >> many thanks
> >>
> >> Paul
> >
> >
> > I sent you a binary by email.
> > This new g_covar of the soon to be release 3.2.0 version also calculates
> > the covariance matrix in a more accurate way.
> >
> > Berk.
> >
> > _________________________________________________________________
> > Protect your PC - get McAfee.com VirusScan Online
> > http://clinic.mcafee.com/clinic/ibuy/campaign.asp?cid=3963
> >
> > _______________________________________________
> > 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.
> >
> >
>
> --
> PLEASE NOTE NEW ADDRESS AND PHONE/FAX NUMBERS
>
> Ruben Martínez-Buey. PhD student.
> Protein Function and Structure
> Centro de Investigaciones Biológicas
> Consejo Superior de Investigaciones Científicas
> C/ Ramiro de Maeztu, 9
> 28040 Madrid (SPAIN)
> phone:34-918373112 ext 4380
> fax: 34-915360432
>
> --__--__--
>
> Message: 10
> From: "Berk Hess" <gmx3 at hotmail.com>
> To: gmx-users at gromacs.org
> Subject: [gmx-users] Re: quick fix for g_covar?
> Date: Tue, 25 Nov 2003 16:49:49 +0100
> Reply-To: gmx-users at gromacs.org
>
> >Hi Berk,
> >Where can I get this new g_covar?
> >Thanks in advance
> >best wishes,
> >Ruben
>
> By getting the cvs code, or by waiting a few weeks for the release of
> Gromacs 3.2.0.
>
> I just remembered that you can obtain the covariance matrix in an ascii file
> using
> g_covar -debug
> (also in Gromacs 3.1)
> Maybe this should be a standard option.
>
> Berk.
>
> _________________________________________________________________
> MSN Search, for accurate results! http://search.msn.nl
>
> --__--__--
>
> Message: 11
> Subject: Re: [gmx-users] Imaging Problem
> From: Ilya Chorny <ichorny at maxwell.compbio.ucsf.edu>
> To: "gmx-users at gromacs.org" <gmx-users at gromacs.org>
> Organization:
> Date: 25 Nov 2003 09:24:28 -0800
> Reply-To: gmx-users at gromacs.org
>
> Could someone please take a look at my posting. I am attempting to do
> umbrella sampling but this is a bug that was supposed to be fixed
> according to the postings. Should I download the CVS version of gromacs?
>
> Ilya
>
> On Mon, 2003-11-24 at 11:48, Ilya Chorny wrote:
> > Hello
> >
> > I ran a distance restraint calculation between two molecules where I
> > kept the distance between two of the atoms fixed. I had some strange
> > results and when I watched the trajectory using VMD I noticed that when
> > one of the molecules left the box it got moved to the other side as one
> > would expect but the distance between the molecules also changed to the
> > geometric distance and not the min image distance. Am I making some
> > mistake in setting up the calculation.
> >
> >
> > Thanks
> >
> > Ilya
> >
> > cpp = /lib/cpp
> > integrator = md
> > constraints = all-bonds
> > dt = 0.002 ; ps !
> > nsteps = 500000 ; total 10 ps.
> > nstcomm = 1
> > nstenergy = 100
> > nstlist = 1
> > coulombtype = PME
> > rlist = .9
> > rcoulomb = .9
> > rvdw = .9
> > Tcoupl = nose-hoover
> > tc-grps = SOL COO AGG
> > tau_t = 0.1 0.1 .1
> > ref_t = 300 300 300
> > ; Energy monitoring
> > ; Pressure coupling is not on
> > Pcoupl = berendsen
> > tau_p = 0.5
> > compressibility = 6.0e-6
> > ref_p = 1.0
> > ; Generate velocites is on at 300 K.
> > gen_vel = yes
> > gen_temp = 300.0
> > gen_seed = 173529
> > ; distance restraints
> > disre = simple
> > disre_weighting = equal
> > nstdisreout = 10
> >
> >
> >
> >
> >
> >
> > _______________________________________________
> > 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.
>
> --__--__--
>
> Message: 12
> Date: Tue, 25 Nov 2003 16:23:41 -0700
> From: Luca Monticelli <lmonti at ucalgary.ca>
> To: gmx-users at gromacs.org
> Cc: gmx-developers at gromacs.org
> Subject: Re: [gmx-users] replica exchange
> Reply-To: gmx-users at gromacs.org
>
> Hi Ilya,
>
> I've been working on a replica exchange
> version of gromacs together with Walter
> Ash (also in Peter Tieleman's group).
> The code seems to be working, but we are
> still testing it; also, we think there
> are still a few things that need to be
> fixed, and we prefer not to release the
> code until we make sure it does not
> contain stupid errors.
> It's not my highest priority project
> (same for Walter), but I think we'll be
> able to release a beta version by the
> end of the year (hopefully).
> Anyway, if you want to use scripts
> (instead of a modified code) it's going
> to be really straightforward.
>
> Cheers,
>
> luca
>
> Ilya Chorny wrote:
> > Has anyone done replica exchange in gromacs. (i.e written the scripts to
> > due replica exchange). It seems like it would be pretty straight forward
> > but I don't want to reinvent the wheel if its already been invented.
> >
> > Thanks
> >
> > Ilya
>
> --
> ___________________________________
>
> Luca Monticelli, PhD
> Department of Biological Sciences
> University of Calgary
> 2500 University Drive NW
> Calgary, AB, T2N 1N4, Canada
> e-mail: lmonti at ucalgary.ca
> Phone: (403) 220-2264
> Fax: (403) 289-9311
> ___________________________________
>
> --__--__--
>
> Message: 13
> Subject: Re: [gmx-users] replica exchange
> From: Ilya Chorny <ichorny at maxwell.compbio.ucsf.edu>
> To: "gmx-users at gromacs.org" <gmx-users at gromacs.org>
> Organization:
> Date: 25 Nov 2003 15:54:19 -0800
> Reply-To: gmx-users at gromacs.org
>
> Hi Luca,
>
> That sounds great. I have not started writing the scripts because my
> simulations are getting good sampling at one temp, but I was thinking
> about future calculations.
>
> Thanks
>
> Ilya
>
>
> On Tue, 2003-11-25 at 15:23, Luca Monticelli wrote:
> > Hi Ilya,
> >
> > I've been working on a replica exchange
> > version of gromacs together with Walter
> > Ash (also in Peter Tieleman's group).
> > The code seems to be working, but we are
> > still testing it; also, we think there
> > are still a few things that need to be
> > fixed, and we prefer not to release the
> > code until we make sure it does not
> > contain stupid errors.
> > It's not my highest priority project
> > (same for Walter), but I think we'll be
> > able to release a beta version by the
> > end of the year (hopefully).
> > Anyway, if you want to use scripts
> > (instead of a modified code) it's going
> > to be really straightforward.
> >
> > Cheers,
> >
> > luca
> >
> >
> >
> > Ilya Chorny wrote:
> > > Has anyone done replica exchange in gromacs. (i.e written the scripts to
> > > due replica exchange). It seems like it would be pretty straight forward
> > > but I don't want to reinvent the wheel if its already been invented.
> > >
> > > Thanks
> > >
> > > Ilya
> >
>
> --__--__--
>
> Message: 14
> Date: Wed, 26 Nov 2003 12:44:09 +1100
> From: Dallas Warren <dallas.warren at vcp.monash.edu.au>
> Subject: Re: [gmx-users] g_rdf
> To: gmx-users at gromacs.org
> Reply-To: gmx-users at gromacs.org
>
> > I have Cl- and Na+ en water, how I can do the rdf
> >to: Oxigen with Cl-, Oxigen with Na+, Hidrogen with Na+, Hidrogen
> >with CL-?
>
> Generate an index file (make_ndx) that has groups of Cl-, Na+, OW and HW1 +
> HW2. Then run g_rdf for each of the pairs of groups you are interested in
> for a given trajectory.
>
> Catch ya,
>
> Dr. Dallas Warren
> Research Fellow
> Department of Pharmaceutical Biology and Pharmacology
> Victorian College of Pharmacy, Monash University
> 381 Royal Parade, Parkville VIC 3010
> dallas.warren at vcp.monash.edu.au
> +61 3 9903 9083
> --------------------------------------------------------------------------
> When the only tool you own is a hammer, every problem begins to resemble a nail.
>
> --__--__--
>
> Message: 15
> From: "wang chuanming" <chuanmingwang at hotmail.com>
> To: gmx-users at gromacs.org
> Date: Wed, 26 Nov 2003 14:05:24 +0800
> Subject: [gmx-users] Problem on processing proteins consisting of two chains
> Reply-To: gmx-users at gromacs.org
>
> Dear all,
> I am a new user of Gromacs.I am trying to do a simulation on a protein
> which consists of two chains(A and B) like HIV PR.Unfortunately, the two
> chains got far away from each other. I found that two itp
> files(protein_A.itp and protein_B.itp) were generated after using pdb2gmx.
> It seems that Gromacs recognizes the two chains as different proteins,but
> they belong to the same molecule indeed.
> How can I resolve the problem? Your experiences on Gromacs will helful
> for me.
>
> _________________________________________________________________
> ÓëÁª»úµÄÅóÓѽøÐн»Á÷£¬ÇëʹÓà MSN Messenger: http://messenger.msn.com/cn
>
> --__--__--
>
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