[gmx-users] DSSP problem
Manik Mayur
manik.mayur at gmail.com
Thu Jun 4 10:32:11 CEST 2009
On Thu, Jun 4, 2009 at 1:40 PM, rituraj purohit <riturajpurohit at gmail.com>wrote:
> Dear mark
> Where i can get the file with permission.
> I downloaded from http://swift.cmbi.kun.nl/gv/dssp/
>
$chmod a+x <path to>/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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> >
> > End of gmx-users Digest, Vol 62, Issue 26
> > *****************************************
> >
>
>
> --
> "The future belongs to those who believe in the beauty of their dreams."
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Manik Mayur
Graduate student
Microfluidics Lab
Dept. of Mechanical Engg.
IIT Kharagpur
INDIA
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