<div class="gmail_quote">On Thu, Jun 4, 2009 at 1:40 PM, rituraj purohit <span dir="ltr"><<a href="mailto:riturajpurohit@gmail.com">riturajpurohit@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Dear mark<br>
Where i can get the file with permission.<br>
I downloaded from <a href="http://swift.cmbi.kun.nl/gv/dssp/" target="_blank">http://swift.cmbi.kun.nl/gv/dssp/</a><br>
</blockquote><br>$chmod a+x <path to>/dssp<br><br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Rituraj<br>
<br>
On 6/4/09, <a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a> <<a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>> wrote:<br>
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> Today's Topics:<br>
><br>
> 1. Re: PME on BlueGene (Mark Abraham)<br>
> 2. about PMF calculation (<a href="mailto:mircial@sjtu.edu.cn">mircial@sjtu.edu.cn</a>)<br>
> 3. Replacing the PRODRG charges (Lucio Ricardo Montero Valenzuela)<br>
> 4. Re: Replacing the PRODRG charges (Mark Abraham)<br>
> 5. how to include ionic strength (amri ta)<br>
> 6. Re: how to include ionic strength (Mark Abraham)<br>
> 7. DSSP problem (rituraj purohit)<br>
> 8. Re: DSSP problem (Mark Abraham)<br>
><br>
><br>
> ----------------------------------------------------------------------<br>
><br>
> Message: 1<br>
> Date: Thu, 04 Jun 2009 11:06:16 +1000<br>
> From: Mark Abraham <<a href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>><br>
> Subject: Re: [gmx-users] PME on BlueGene<br>
> To: Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>
> Message-ID: <<a href="mailto:4A271E08.2090806@anu.edu.au">4A271E08.2090806@anu.edu.au</a>><br>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed<br>
><br>
> Jakob Wohlert wrote:<br>
> > Mark Abraham wrote:<br>
> >> Jakob Wohlert wrote:<br>
> >>> Hi,<br>
> >>><br>
> >>> I'm trying to compile Gromacs 4.0.4 for BlueGene/P, and using the<br>
> >>> configuration options from the wiki I have succeeded insofar that I<br>
> >>> have a<br>
> >>> working program as long as I don't use PME.<br>
> >>><br>
> >>> I have tried many different variants of fftw - 2.1.5, 3.2.1, single<br>
> >>> precision, double precision, different compiler optimizations and so on,<br>
> >>> but it all ends the same: mdrun getting stuck somewhere in the<br>
> >>> initialization process.<br>
> >>><br>
> >>> However, by using the built in fft library FFTPACK instead of FFTW, PME<br>
> >>> will work, but that is not really an alternative.<br>
> >>><br>
> >>> In at least a few cases I have been able to pinpoint the location<br>
> >>> where it<br>
> >>> hangs - it's in pme.c, subroutine pme_dd_sendrecv. The program calls<br>
> >>> MPI_Sendrecv, but then nothing else happens as far as I can tell.<br>
> >>><br>
> >>> I'm confused and I have sort of ran out of ideas right now. Has anyone<br>
> >>> else encountered a problem like this, or has anyone any suggestions<br>
> >>> how to<br>
> >>> proceed from here?<br>
> > Thanks for your answer!<br>
> ><br>
> >> That looks to me like the separate PME nodes are dying through some<br>
> >> linking problem and the problem is only manifest on node 0 when its<br>
> >> sendrecv doesn't complete. Forcing mdrun -npme 0 may confirm this when<br>
> >> all the nodes die at the first point they refer to a symbol in the FFT<br>
> >> library.<br>
> >><br>
> >> Otherwise, looking at warnings/errors from the linker will be required.<br>
> > Ok, can you be a little more specific? Do you mean when compiling fftw,<br>
> > gromacs or both? I'm not very experienced with these kind of things.<br>
><br>
> GROMACS links with the FFTW library, so there ought to be warnings of<br>
> potential problems at link time, i.e. the final stage of a GROMACS "make<br>
> mdrun" (having started with a clean configuration, either freshly<br>
> unpacked or after "make clean"). The last 100 or so lines of the output<br>
> of "make mdrun" should have any relevant data.<br>
><br>
> >> Are you compiling an FFT library version for the back end, or the<br>
> >> front end?<br>
> > I'm trying to get it to work on the back end, on the front end it works<br>
> > fine! (So, I have fftw libraries for both).<br>
><br>
> My BG/L FFTW-3.2 configure line is<br>
><br>
> ../configure --prefix /hpc/home/mja163/progs CC=blrts_xlc --host=powerpc<br>
> --build=ppc64 CFLAGS=-qbgl -qarch=440d -qtune=440 -qnoautoconfig -O5<br>
> --disable-fortran --enable-float<br>
><br>
> but you may need to tweak that for BG/P for all I know. Let me know<br>
> when/if something works and I'll update the wiki.<br>
><br>
> Mark<br>
><br>
><br>
> ------------------------------<br>
><br>
> Message: 2<br>
> Date: Thu, 04 Jun 2009 13:56:51 +0800<br>
> From: <a href="mailto:mircial@sjtu.edu.cn">mircial@sjtu.edu.cn</a><br>
> Subject: [gmx-users] about PMF calculation<br>
> To: <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
> Message-ID: <<a href="mailto:20090604135651.2wdhcqo28csw8kc8@webmail1.sjtu.edu.cn">20090604135651.2wdhcqo28csw8kc8@webmail1.sjtu.edu.cn</a>><br>
> Content-Type: text/plain; charset=GB2312; DelSp="Yes"; format="flowed"<br>
><br>
> Dear All:<br>
><br>
> I want to do some PMF (Potenial of Mean Force) calculation by<br>
> AFM pulling method using the pull code to study the unbinding of a<br>
> protein and a ligand.<br>
><br>
> I want pull the ligand from its binding site and calculate the<br>
> PMF of the procedure, does it possible?<br>
><br>
> I have read the user manual about PMF calculation carefully, but<br>
> still not clear how to do . Does anyone have any tutorial about how to<br>
> do this kind of calculation or any published papers doing this things?<br>
> anyhelp is greatly appreciate!<br>
><br>
><br>
> Best Wishes<br>
> R-X Gu<br>
><br>
><br>
><br>
> ------------------------------<br>
><br>
> Message: 3<br>
> Date: Thu, 04 Jun 2009 01:24:32 -0500<br>
> From: Lucio Ricardo Montero Valenzuela <<a href="mailto:lucioric@ibt.unam.mx">lucioric@ibt.unam.mx</a>><br>
> Subject: [gmx-users] Replacing the PRODRG charges<br>
> To: <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
> Message-ID: <<a href="mailto:1244096672.4a2768a0e40d0@webmail.ibt.unam.mx">1244096672.4a2768a0e40d0@webmail.ibt.unam.mx</a>><br>
> Content-Type: text/plain; charset=ISO-8859-1<br>
><br>
> I want to run a MD in an unparameterized molecule similar to adenine. I can get<br>
> the approximated parameters in PRODRG. But I have read that PRODRG not always<br>
> give the correct charge. Is it a good idea to replace that charges using the<br>
> charges given with the R.E.D.vIII using ESP-A1 (suitable for AMBER, GLYCAM and<br>
> OPLS forcefields)?. Or will it be mixing forcefields?.<br>
><br>
> Lucio Ricardo Montero Valenzuela<br>
> Instituto de Biotecnologia, UNAM<br>
> Departamento de Biologia Molecular de Plantas<br>
> Av. Universidad 2001, Col. Chamilpa<br>
> Cuernavaca 62210<br>
> Mexico<br>
><br>
> ----------------------------------------------------------------<br>
> Este mensaje fue enviado desde el servidor Webmail del Instituto de Biotecnologia.<br>
><br>
><br>
> ------------------------------<br>
><br>
> Message: 4<br>
> Date: Thu, 04 Jun 2009 16:29:03 +1000<br>
> From: Mark Abraham <<a href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>><br>
> Subject: Re: [gmx-users] Replacing the PRODRG charges<br>
> To: Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>
> Message-ID: <<a href="mailto:4A2769AF.6000808@anu.edu.au">4A2769AF.6000808@anu.edu.au</a>><br>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed<br>
><br>
> Lucio Ricardo Montero Valenzuela wrote:<br>
> > I want to run a MD in an unparameterized molecule similar to adenine. I can get<br>
> > the approximated parameters in PRODRG. But I have read that PRODRG not always<br>
> > give the correct charge. Is it a good idea to replace that charges using the<br>
> > charges given with the R.E.D.vIII using ESP-A1 (suitable for AMBER, GLYCAM and<br>
> > OPLS forcefields)?. Or will it be mixing forcefields?.<br>
><br>
> That depends on your target forcefield for your MD.<br>
><br>
> Mark<br>
><br>
><br>
> ------------------------------<br>
><br>
> Message: 5<br>
> Date: Thu, 4 Jun 2009 12:27:00 +0530 (IST)<br>
> From: amri ta <<a href="mailto:amrita0092002@yahoo.co.in">amrita0092002@yahoo.co.in</a>><br>
> Subject: [gmx-users] how to include ionic strength<br>
> To: <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
> Message-ID: <<a href="mailto:418624.33836.qm@web8708.mail.in.yahoo.com">418624.33836.qm@web8708.mail.in.yahoo.com</a>><br>
> Content-Type: text/plain; charset="iso-8859-1"<br>
><br>
> Dear gromacs users,<br>
><br>
> 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.<br>
><br>
> Thanks in advance.<br>
> Amrita Paul<br>
><br>
><br>
><br>
><br>
> Cricket on your mind? Visit the ultimate cricket website. Enter <a href="http://beta.cricket.yahoo.com" target="_blank">http://beta.cricket.yahoo.com</a><br>
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><br>
> ------------------------------<br>
><br>
> Message: 6<br>
> Date: Thu, 04 Jun 2009 17:09:35 +1000<br>
> From: Mark Abraham <<a href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>><br>
> Subject: Re: [gmx-users] how to include ionic strength<br>
> To: Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>
> Message-ID: <<a href="mailto:4A27732F.1020303@anu.edu.au">4A27732F.1020303@anu.edu.au</a>><br>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed<br>
><br>
> amri ta wrote:<br>
> > Dear gromacs users,<br>
> ><br>
> > I am simulating a protein which works in salt solution within cell. I<br>
> > have to include 4M salt (say, NaCl) to the simulation box. How can i<br>
> > include such ionic strength? Please outline me the procedure.<br>
><br>
> If you do some tutorial material, you will find out the procedure for<br>
> adding ions. Finding out how many ions to add is for you to calculate :-)<br>
><br>
> Mark<br>
><br>
><br>
> ------------------------------<br>
><br>
> Message: 7<br>
> Date: Thu, 4 Jun 2009 12:52:32 +0530<br>
> From: rituraj purohit <<a href="mailto:riturajpurohit@gmail.com">riturajpurohit@gmail.com</a>><br>
> Subject: [gmx-users] DSSP problem<br>
> To: <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
> Message-ID:<br>
> <<a href="mailto:685cca3f0906040022j73103651p972ec3922736edc9@mail.gmail.com">685cca3f0906040022j73103651p972ec3922736edc9@mail.gmail.com</a>><br>
> Content-Type: text/plain; charset=ISO-8859-1<br>
><br>
> Dear all<br>
> I want ti install DSSP for visualization of secondary structure in<br>
> gromacs analysis.<br>
> I am doing following procedure..<br>
> Copy the executable "dsspcmbi" to /usr/bin or /usr/local/bin<br>
> ln -s dsspcmbi dssp<br>
> And running it for my Pdb like that....<br>
> dssp file.pdb file.dssp<br>
><br>
> BUt I am getting error "Permission Denied" even i m super user for the<br>
> machine (root).<br>
><br>
> [root@localhost ~]# dssp<br>
> bash: /usr/local/bin/dssp: Permission denied<br>
> [root@localhost ~]#<br>
><br>
> Plaese any body tell the solution for this problem...<br>
><br>
> Regard<br>
> Rituraj<br>
><br>
><br>
><br>
> --<br>
> "The future belongs to those who believe in the beauty of their dreams."<br>
><br>
><br>
> ------------------------------<br>
><br>
> Message: 8<br>
> Date: Thu, 04 Jun 2009 17:28:13 +1000<br>
> From: Mark Abraham <<a href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>><br>
> Subject: Re: [gmx-users] DSSP problem<br>
> To: Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>
> Message-ID: <<a href="mailto:4A27778D.1060506@anu.edu.au">4A27778D.1060506@anu.edu.au</a>><br>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed<br>
><br>
> rituraj purohit wrote:<br>
> > Dear all<br>
> > I want ti install DSSP for visualization of secondary structure in<br>
> > gromacs analysis.<br>
> > I am doing following procedure..<br>
> > Copy the executable "dsspcmbi" to /usr/bin or /usr/local/bin<br>
> > ln -s dsspcmbi dssp<br>
> > And running it for my Pdb like that....<br>
> > dssp file.pdb file.dssp<br>
> ><br>
> > BUt I am getting error "Permission Denied" even i m super user for the<br>
> > machine (root).<br>
> ><br>
> > [root@localhost ~]# dssp<br>
> > bash: /usr/local/bin/dssp: Permission denied<br>
> > [root@localhost ~]#<br>
> ><br>
> > Plaese any body tell the solution for this problem...<br>
><br>
> You may still need execute permissions on the original executable. You<br>
> should not ever be running as root when not installing software or<br>
> maintaining the system.<br>
><br>
> Mark<br>
><br>
><br>
> ------------------------------<br>
><br>
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> End of gmx-users Digest, Vol 62, Issue 26<br>
> *****************************************<br>
><br>
<br>
<br>
--<br>
"The future belongs to those who believe in the beauty of their dreams."<br>
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</blockquote></div><br clear="all">Manik Mayur<br>Graduate student<br>Microfluidics Lab<br>Dept. of Mechanical Engg.<br>IIT Kharagpur<br>INDIA<br>
<br>