[gmx-users] DSSP problem
rituraj purohit
riturajpurohit at gmail.com
Thu Jun 4 10:10:18 CEST 2009
Dear mark
Where i can get the file with permission.
I downloaded from http://swift.cmbi.kun.nl/gv/dssp/
Rituraj
On 6/4/09, gmx-users-request at gromacs.org <gmx-users-request at gromacs.org> wrote:
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> Today's Topics:
>
> 1. Re: PME on BlueGene (Mark Abraham)
> 2. about PMF calculation (mircial at sjtu.edu.cn)
> 3. Replacing the PRODRG charges (Lucio Ricardo Montero Valenzuela)
> 4. Re: Replacing the PRODRG charges (Mark Abraham)
> 5. how to include ionic strength (amri ta)
> 6. Re: how to include ionic strength (Mark Abraham)
> 7. DSSP problem (rituraj purohit)
> 8. Re: DSSP problem (Mark Abraham)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Thu, 04 Jun 2009 11:06:16 +1000
> From: Mark Abraham <Mark.Abraham at anu.edu.au>
> Subject: Re: [gmx-users] PME on BlueGene
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <4A271E08.2090806 at anu.edu.au>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> Jakob Wohlert wrote:
> > Mark Abraham wrote:
> >> Jakob Wohlert wrote:
> >>> Hi,
> >>>
> >>> I'm trying to compile Gromacs 4.0.4 for BlueGene/P, and using the
> >>> configuration options from the wiki I have succeeded insofar that I
> >>> have a
> >>> working program as long as I don't use PME.
> >>>
> >>> I have tried many different variants of fftw - 2.1.5, 3.2.1, single
> >>> precision, double precision, different compiler optimizations and so on,
> >>> but it all ends the same: mdrun getting stuck somewhere in the
> >>> initialization process.
> >>>
> >>> However, by using the built in fft library FFTPACK instead of FFTW, PME
> >>> will work, but that is not really an alternative.
> >>>
> >>> In at least a few cases I have been able to pinpoint the location
> >>> where it
> >>> hangs - it's in pme.c, subroutine pme_dd_sendrecv. The program calls
> >>> MPI_Sendrecv, but then nothing else happens as far as I can tell.
> >>>
> >>> I'm confused and I have sort of ran out of ideas right now. Has anyone
> >>> else encountered a problem like this, or has anyone any suggestions
> >>> how to
> >>> proceed from here?
> > Thanks for your answer!
> >
> >> That looks to me like the separate PME nodes are dying through some
> >> linking problem and the problem is only manifest on node 0 when its
> >> sendrecv doesn't complete. Forcing mdrun -npme 0 may confirm this when
> >> all the nodes die at the first point they refer to a symbol in the FFT
> >> library.
> >>
> >> Otherwise, looking at warnings/errors from the linker will be required.
> > Ok, can you be a little more specific? Do you mean when compiling fftw,
> > gromacs or both? I'm not very experienced with these kind of things.
>
> GROMACS links with the FFTW library, so there ought to be warnings of
> potential problems at link time, i.e. the final stage of a GROMACS "make
> mdrun" (having started with a clean configuration, either freshly
> unpacked or after "make clean"). The last 100 or so lines of the output
> of "make mdrun" should have any relevant data.
>
> >> Are you compiling an FFT library version for the back end, or the
> >> front end?
> > I'm trying to get it to work on the back end, on the front end it works
> > fine! (So, I have fftw libraries for both).
>
> My BG/L FFTW-3.2 configure line is
>
> ../configure --prefix /hpc/home/mja163/progs CC=blrts_xlc --host=powerpc
> --build=ppc64 CFLAGS=-qbgl -qarch=440d -qtune=440 -qnoautoconfig -O5
> --disable-fortran --enable-float
>
> but you may need to tweak that for BG/P for all I know. Let me know
> when/if something works and I'll update the wiki.
>
> Mark
>
>
> ------------------------------
>
> Message: 2
> Date: Thu, 04 Jun 2009 13:56:51 +0800
> From: mircial at sjtu.edu.cn
> Subject: [gmx-users] about PMF calculation
> To: gmx-users at gromacs.org
> Message-ID: <20090604135651.2wdhcqo28csw8kc8 at webmail1.sjtu.edu.cn>
> Content-Type: text/plain; charset=GB2312; DelSp="Yes"; format="flowed"
>
> Dear All:
>
> I want to do some PMF (Potenial of Mean Force) calculation by
> AFM pulling method using the pull code to study the unbinding of a
> protein and a ligand.
>
> I want pull the ligand from its binding site and calculate the
> PMF of the procedure, does it possible?
>
> I have read the user manual about PMF calculation carefully, but
> still not clear how to do . Does anyone have any tutorial about how to
> do this kind of calculation or any published papers doing this things?
> anyhelp is greatly appreciate!
>
>
> Best Wishes
> R-X Gu
>
>
>
> ------------------------------
>
> Message: 3
> Date: Thu, 04 Jun 2009 01:24:32 -0500
> From: Lucio Ricardo Montero Valenzuela <lucioric at ibt.unam.mx>
> Subject: [gmx-users] Replacing the PRODRG charges
> To: gmx-users at gromacs.org
> Message-ID: <1244096672.4a2768a0e40d0 at webmail.ibt.unam.mx>
> Content-Type: text/plain; charset=ISO-8859-1
>
> I want to run a MD in an unparameterized molecule similar to adenine. I can get
> the approximated parameters in PRODRG. But I have read that PRODRG not always
> give the correct charge. Is it a good idea to replace that charges using the
> charges given with the R.E.D.vIII using ESP-A1 (suitable for AMBER, GLYCAM and
> OPLS forcefields)?. Or will it be mixing forcefields?.
>
> Lucio Ricardo Montero Valenzuela
> Instituto de Biotecnologia, UNAM
> Departamento de Biologia Molecular de Plantas
> Av. Universidad 2001, Col. Chamilpa
> Cuernavaca 62210
> Mexico
>
> ----------------------------------------------------------------
> Este mensaje fue enviado desde el servidor Webmail del Instituto de Biotecnologia.
>
>
> ------------------------------
>
> Message: 4
> Date: Thu, 04 Jun 2009 16:29:03 +1000
> From: Mark Abraham <Mark.Abraham at anu.edu.au>
> Subject: Re: [gmx-users] Replacing the PRODRG charges
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <4A2769AF.6000808 at anu.edu.au>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> Lucio Ricardo Montero Valenzuela wrote:
> > I want to run a MD in an unparameterized molecule similar to adenine. I can get
> > the approximated parameters in PRODRG. But I have read that PRODRG not always
> > give the correct charge. Is it a good idea to replace that charges using the
> > charges given with the R.E.D.vIII using ESP-A1 (suitable for AMBER, GLYCAM and
> > OPLS forcefields)?. Or will it be mixing forcefields?.
>
> That depends on your target forcefield for your MD.
>
> Mark
>
>
> ------------------------------
>
> Message: 5
> Date: Thu, 4 Jun 2009 12:27:00 +0530 (IST)
> From: amri ta <amrita0092002 at yahoo.co.in>
> Subject: [gmx-users] how to include ionic strength
> To: gmx-users at gromacs.org
> Message-ID: <418624.33836.qm at web8708.mail.in.yahoo.com>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Dear gromacs users,
>
> I am simulating a protein which works in salt solution within cell. I have to include 4M salt (say, NaCl) to the simulation box. How can i include such ionic strength? Please outline me the procedure.
>
> Thanks in advance.
> Amrita Paul
>
>
>
>
> Cricket on your mind? Visit the ultimate cricket website. Enter http://beta.cricket.yahoo.com
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> ------------------------------
>
> Message: 6
> Date: Thu, 04 Jun 2009 17:09:35 +1000
> From: Mark Abraham <Mark.Abraham at anu.edu.au>
> Subject: Re: [gmx-users] how to include ionic strength
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <4A27732F.1020303 at anu.edu.au>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> amri ta wrote:
> > Dear gromacs users,
> >
> > I am simulating a protein which works in salt solution within cell. I
> > have to include 4M salt (say, NaCl) to the simulation box. How can i
> > include such ionic strength? Please outline me the procedure.
>
> If you do some tutorial material, you will find out the procedure for
> adding ions. Finding out how many ions to add is for you to calculate :-)
>
> Mark
>
>
> ------------------------------
>
> Message: 7
> Date: Thu, 4 Jun 2009 12:52:32 +0530
> From: rituraj purohit <riturajpurohit at gmail.com>
> Subject: [gmx-users] DSSP problem
> To: gmx-users at gromacs.org
> Message-ID:
> <685cca3f0906040022j73103651p972ec3922736edc9 at mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
>
> Dear all
> I want ti install DSSP for visualization of secondary structure in
> gromacs analysis.
> I am doing following procedure..
> Copy the executable "dsspcmbi" to /usr/bin or /usr/local/bin
> ln -s dsspcmbi dssp
> And running it for my Pdb like that....
> dssp file.pdb file.dssp
>
> BUt I am getting error "Permission Denied" even i m super user for the
> machine (root).
>
> [root at localhost ~]# dssp
> bash: /usr/local/bin/dssp: Permission denied
> [root at localhost ~]#
>
> Plaese any body tell the solution for this problem...
>
> Regard
> Rituraj
>
>
>
> --
> "The future belongs to those who believe in the beauty of their dreams."
>
>
> ------------------------------
>
> Message: 8
> Date: Thu, 04 Jun 2009 17:28:13 +1000
> From: Mark Abraham <Mark.Abraham at anu.edu.au>
> Subject: Re: [gmx-users] DSSP problem
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <4A27778D.1060506 at anu.edu.au>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> rituraj purohit wrote:
> > Dear all
> > I want ti install DSSP for visualization of secondary structure in
> > gromacs analysis.
> > I am doing following procedure..
> > Copy the executable "dsspcmbi" to /usr/bin or /usr/local/bin
> > ln -s dsspcmbi dssp
> > And running it for my Pdb like that....
> > dssp file.pdb file.dssp
> >
> > BUt I am getting error "Permission Denied" even i m super user for the
> > machine (root).
> >
> > [root at localhost ~]# dssp
> > bash: /usr/local/bin/dssp: Permission denied
> > [root at localhost ~]#
> >
> > Plaese any body tell the solution for this problem...
>
> You may still need execute permissions on the original executable. You
> should not ever be running as root when not installing software or
> maintaining the system.
>
> Mark
>
>
> ------------------------------
>
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