[gmx-users] Re: gmx-users Digest, Vol 85, Issue 61
Maria Hamilton
hamilton.maria39 at gmail.com
Mon May 9 07:40:57 CEST 2011
Hi Dallas
You said that
"Easiest way is probably set up the appropriate sized box for molecule 2,
randomly distributed molecule 3 in appropriate number through it (genbox),
then solvate that box with molecule 2, then combine that box with solvated
box containing molecule 1."
How can I combine the two different box?Do you know any tutorial for this?
Thanks alot
Maria
On Mon, May 9, 2011 at 5:54 AM, <gmx-users-request at gromacs.org> wrote:
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> Today's Topics:
>
> 1. sphere around a protein (shivangi nangia)
> 2. Re: sphere around a protein (Justin A. Lemkul)
> 3. RE: gmx-users Digest, Vol 85, Issue 53 (Ryan S Davis (rsdavis1))
> 4. RE: liquid/liquid (Dallas Warren)
> 5. Re: sphere around a protein (shivangi nangia)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Sun, 8 May 2011 16:13:33 -0400
> From: shivangi nangia <shivangi.nangia at gmail.com>
> Subject: [gmx-users] sphere around a protein
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <BANLkTin3xJKSGRLuckLhqba8YZ=MKVs1kA at mail.gmail.com>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Hi Justin and other gmx-users,
>
> I want to make a sphere around a protein (5nm).with Li ions and anions.
>
> Justin, as you had suggested to use genbox -shell option, I tried using it
> but i realized that since my protein is a long tube like structure, the
> shell option generated a cyclinder around the protein.
>
> The solvent around the protein is 1:1 water-methanol (pre-prepared mixture
> n
> a gro file)
>
> If I try to start with a ion and solvate it with my solvent (1:1 water
> methanol) using -shell option, I do get a sphere but then I am unable to
> insert the protein in the system.
>
> Is there another feasible route to get to my desired configuration of the
> system ?
>
> Thanks in advance
>
>
> Best,
> SN
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> ------------------------------
>
> Message: 2
> Date: Sun, 08 May 2011 17:12:33 -0400
> From: "Justin A. Lemkul" <jalemkul at vt.edu>
> Subject: Re: [gmx-users] sphere around a protein
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <4DC70741.8080209 at vt.edu>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
>
>
> shivangi nangia wrote:
> > Hi Justin and other gmx-users,
> >
> > I want to make a sphere around a protein (5nm).with Li ions and anions.
> >
> > Justin, as you had suggested to use genbox -shell option, I tried using
> > it but i realized that since my protein is a long tube like structure,
> > the shell option generated a cyclinder around the protein.
> >
> > The solvent around the protein is 1:1 water-methanol (pre-prepared
> > mixture n a gro file)
> >
> > If I try to start with a ion and solvate it with my solvent (1:1 water
> > methanol) using -shell option, I do get a sphere but then I am unable to
> > insert the protein in the system.
> >
>
> And why not?
>
> genbox -cp protein.gro -cs sphere.gro
>
> should do exactly what you want, provided the sphere is large enough for
> the
> protein.
>
> -Justin
>
> > Is there another feasible route to get to my desired configuration of
> > the system ?
> >
> > Thanks in advance
> >
> >
> > Best,
> > SN
> >
> >
> >
>
> --
> ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
>
>
> ------------------------------
>
> Message: 3
> Date: Sun, 8 May 2011 18:10:22 -0500
> From: "Ryan S Davis (rsdavis1)" <rsdavis1 at memphis.edu>
> Subject: [gmx-users] RE: gmx-users Digest, Vol 85, Issue 53
> To: "gmx-users at gromacs.org" <gmx-users at gromacs.org>
> Message-ID:
> <
> 6A7C9BBA12F23B478D0E40C0F6B8D4E87FCD23147C at itexbe11.uom.memphis.edu>
> Content-Type: text/plain; charset="us-ascii"
>
> I am not sure if I replied to this thread correctly, but anyway.
>
> I tried the things you guys suggested, but I still cant get it to work.
> You were right $HOME does have a slash in front but I am not actually using
> that variable, just used it in the mailing list for convience, sorry.
>
> I reinstalled the libraries, just to make sure everything went well.
> So, here is what happens when I list out the library tree from my home
> directory and try to run the test code
>
> $ ls -R /home/rsdavis1/apps/xdrfile/
>
> /home/rsdavis1/apps/xdrfile/:
> bin include lib
>
> /home/rsdavis1/apps/xdrfile/bin:
> trr2xtc
>
> /home/rsdavis1/apps/xdrfile/include:
> xdrfile
>
> /home/rsdavis1/apps/xdrfile/include/xdrfile:
> xdrfile.h xdrfile_trr.h xdrfile_xtc.h
>
> /home/rsdavis1/apps/xdrfile/lib:
> libxdrfile.a libxdrfile.la
>
> $
> $
> $ icpc -I/home/rsdavis1/apps/xdrfile/include/xdrfile/
> -L/home/rsdavis1/apps/xdrfile/lib/ test.cpp -lxdrfile
>
> /tmp/icpcUuD5jZ.o: In function `main':
> test.cpp:(.text+0x33): undefined reference to
> `read_xtc_natoms(char*, int*)'
> $
>
>
>
> and, again, test.cpp is just
>
> 1 #include "xdrfile_xtc.h"
> 2
> 3 int main()
> 4 {
> 5
> 6 int natoms;
> 7 read_xtc_natoms("traj.xtc",&natoms);
> 8 return 0;
> 9
> 10 }
>
> The compiler is finding the ".h" file from the include because when I
> specify the wrong function arguments, it complains about it.
> But, I guess it still isnt seeing the library.
> Also, I tried compiling after appending the LIBDIR to my LD_LIBRARY_PATH
> and LD_RUN_PATH, neither worked.
>
>
> Message: 1
> Date: Fri, 6 May 2011 22:31:23 -0500
> From: "Ryan S Davis (rsdavis1)" <rsdavis1 at memphis.edu>
> Subject: [gmx-users] Using the XTC library
> To: "gmx-users at gromacs.org" <gmx-users at gromacs.org>
> Message-ID:
> <
> 6A7C9BBA12F23B478D0E40C0F6B8D4E87FCD231479 at itexbe11.uom.memphis.edu>
> Content-Type: text/plain; charset="us-ascii"
>
> I am trying to use the XTC library in my code but I am just not good at
> this stuff.
> http://www.gromacs.org/Developer_Zone/Programming_Guide/XTC_Library
>
>
> I installed using
> ./configure --prefix=/$HOME/apps/xdrfile
> make install
>
> everything seemed to go well and the make check said everything passed.
>
> So then I try a test code
>
> 1 #include <iostream>
> 2 #include "xdrfile_xtc.h"
> 3 using namespace std;
> 4
> 5 int main()
> 6 {
> 7
> 8 int natoms;
> 9 read_xtc_natoms("traj.xtc", &natoms);
> 10 return 0;
> 11 }
>
> and I compile with
>
> icc -I/$HOME/apps/xdrfile/include/xdrfile -L/$HOME/apps/xdrfile/lib/
> test.cpp
>
> and i get an error saying...
>
> undefined reference to 'read_xtc_natoms(char *, int*)'
>
> I am sure that I am doing something stupid. I tried a C compiler and
> linking to few other random places but, like I said, this stuff (installing
> libraries and linking) is new to me.
> Please help.
>
> Thanks
> Ryan
>
> ------------------------------
>
> Message: 2
> Date: Sat, 07 May 2011 13:55:26 +1000
> From: Mark Abraham <Mark.Abraham at anu.edu.au>
> Subject: Re: [gmx-users] Using the XTC library
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <4DC4C2AE.6090505 at anu.edu.au>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> On 7/05/2011 1:31 PM, Ryan S Davis (rsdavis1) wrote:
> > I am trying to use the XTC library in my code but I am just not good at
> this stuff.
> > http://www.gromacs.org/Developer_Zone/Programming_Guide/XTC_Library
> >
> >
> > I installed using
> > ./configure --prefix=/$HOME/apps/xdrfile
>
> This might not be the problem, but the HOME environment variable here
> and below will normally start with a slash, and so you should not
> preface it with another.
>
> > make install
> >
> > everything seemed to go well and the make check said everything passed.
> >
> > So then I try a test code
> >
> > 1 #include<iostream>
> > 2 #include "xdrfile_xtc.h"
> > 3 using namespace std;
> > 4
> > 5 int main()
> > 6 {
> > 7
> > 8 int natoms;
> > 9 read_xtc_natoms("traj.xtc",&natoms);
> > 10 return 0;
> > 11 }
> >
> > and I compile with
> >
> > icc -I/$HOME/apps/xdrfile/include/xdrfile -L/$HOME/apps/xdrfile/lib/
> test.cpp
> >
> > and i get an error saying...
> >
> > undefined reference to 'read_xtc_natoms(char *, int*)'
> >
> > I am sure that I am doing something stupid. I tried a C compiler and
> linking to few other random places but, like I said, this stuff (installing
> libraries and linking) is new to me.
> > Please help.
>
> icc -I$HOME/apps/xdrfile/include/xdrfile test.cpp
>
> will find $HOME/apps/xdrfile/include/xdrfile/xdrfile_xtc.h
>
> Mark
>
>
>
>
> Message: 4
> Date: Fri, 06 May 2011 22:22:04 -0700
> From: "Joshua L. Phillips" <jphillips7 at ucmerced.edu>
> Subject: Re: [gmx-users] Using the XTC library
> To: gmx-users at gromacs.org
> Message-ID: <1304745725.16113.32.camel at onesiphorus.mercedcapoeira.com>
> Content-Type: text/plain; charset="UTF-8"
>
> You will need to link with the library as well (-lxdrfile)
>
> Something like the following should work (if the paths that you provided
> are correct):
>
> icpc -I$HOME/apps/xdrfile/include/xdrfile \
> -L$HOME/apps/xdrfile/lib test.cpp -o test -lxdrfile
>
> (Since, this is C++ code, then you should be using icpc instead of
> icc...)
>
> -- Josh
>
> On Sat, 2011-05-07 at 13:55 +1000, Mark Abraham wrote:
> > On 7/05/2011 1:31 PM, Ryan S Davis (rsdavis1) wrote:
> > > I am trying to use the XTC library in my code but I am just not good at
> this stuff.
> > > http://www.gromacs.org/Developer_Zone/Programming_Guide/XTC_Library
> > >
> > >
> > > I installed using
> > > ./configure --prefix=/$HOME/apps/xdrfile
> >
> > This might not be the problem, but the HOME environment variable here
> > and below will normally start with a slash, and so you should not
> > preface it with another.
> >
> > > make install
> > >
> > > everything seemed to go well and the make check said everything passed.
> > >
> > > So then I try a test code
> > >
> > > 1 #include<iostream>
> > > 2 #include "xdrfile_xtc.h"
> > > 3 using namespace std;
> > > 4
> > > 5 int main()
> > > 6 {
> > > 7
> > > 8 int natoms;
> > > 9 read_xtc_natoms("traj.xtc",&natoms);
> > > 10 return 0;
> > > 11 }
> > >
> > > and I compile with
> > >
> > > icc -I/$HOME/apps/xdrfile/include/xdrfile -L/$HOME/apps/xdrfile/lib/
> test.cpp
> > >
> > > and i get an error saying...
> > >
> > > undefined reference to 'read_xtc_natoms(char *, int*)'
> > >
> > > I am sure that I am doing something stupid. I tried a C compiler and
> linking to few other random places but, like I said, this stuff (installing
> libraries and linking) is new to me.
> > > Please help.
> >
> > icc -I$HOME/apps/xdrfile/include/xdrfile test.cpp
> >
> > will find $HOME/apps/xdrfile/include/xdrfile/xdrfile_xtc.h
> >
> > Mark
>
> --
> Joshua L. Phillips
> Ph.D. Candidate - School of Engineering
> University of California, Merced
> jphillips7 at ucmerced.edu
>
>
>
> ------------------------------
>
> Message: 4
> Date: Sun, 08 May 2011 23:51:40 +0000
> From: Dallas Warren <Dallas.Warren at monash.edu>
> Subject: RE: [gmx-users] liquid/liquid
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID:
> <F625AF4746B3A74DACFF00F6F65BECCB0C8E4066 at vPRK-MBX-01.vcp.local>
> Content-Type: text/plain; charset="us-ascii"
>
> Easiest way is probably set up the appropriate sized box for molecule 2,
> randomly distributed molecule 3 in appropriate number through it (genbox),
> then solvate that box with molecule 2, then combine that box with solvated
> box containing molecule 1.
>
> Catch ya,
>
> Dr. Dallas Warren
> Medicinal Chemistry and Drug Action
> Monash Institute of Pharmaceutical Sciences, Monash University
> 381 Royal Parade, Parkville VIC 3010
> dallas.warren at monash.edu
> +61 3 9903 9304
> ---------------------------------
> When the only tool you own is a hammer, every problem begins to resemble a
> nail.
>
> From: gmx-users-bounces at gromacs.org [mailto:gmx-users-bounces at gromacs.org]
> On Behalf Of Maria Hamilton
> Sent: Saturday, 7 May 2011 6:04 PM
> To: gmx-users at gromacs.org
> Subject: [gmx-users] liquid/liquid
>
> Hi all
>
> I want to simulate a liquid/liquid interface. After construction one of
> them in one side of the box and the other in the another side, I want to all
> some other molecules randomly in one of them. What should I do?
>
> Would you please help me?
>
> Thanks alot
>
> Maria
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> ------------------------------
>
> Message: 5
> Date: Sun, 8 May 2011 21:23:26 -0400
> From: shivangi nangia <shivangi.nangia at gmail.com>
> Subject: Re: [gmx-users] sphere around a protein
> To: jalemkul at vt.edu, Discussion list for GROMACS users
> <gmx-users at gromacs.org>
> Message-ID: <BANLkTimbHghPcBz6nBUHnBU83t-frDUaEQ at mail.gmail.com>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Hello,
>
> Thanks Justin, I am getting somewhere but still running into problems.
>
> Okay, I have a 6 nm sphere (one Li ion surrounded by 1:1 water-methanol
> mixture) in 12 nm box.
> I did the following:
> editconf -f 1li.gro -c -box 12 12 12 -o onlyli.gro
> genbox -cp onlyli.gro -cs mix.gro -shell 6 -o li_sol.gro
>
>
> Then, used genbox -cp protein.gro -cs sphere.gro
> with only 1 molecule of histidine I get the same error as with
> polyhistidine
> ( 20 )
>
> Fatal error:
> One of the box vectors has become shorter than twice the cut-off length or
> box_yy-|box_zy| or box_zz has become smaller than the cut-off.
>
> How can I resolve this?
>
> help needed.
>
> Thanks,
> SN
>
> On Sun, May 8, 2011 at 5:12 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>
> >
> >
> > shivangi nangia wrote:
> >
> >> Hi Justin and other gmx-users,
> >>
> >> I want to make a sphere around a protein (5nm).with Li ions and anions.
> >>
> >> Justin, as you had suggested to use genbox -shell option, I tried using
> it
> >> but i realized that since my protein is a long tube like structure, the
> >> shell option generated a cyclinder around the protein.
> >>
> >> The solvent around the protein is 1:1 water-methanol (pre-prepared
> mixture
> >> n a gro file)
> >>
> >> If I try to start with a ion and solvate it with my solvent (1:1 water
> >> methanol) using -shell option, I do get a sphere but then I am unable to
> >> insert the protein in the system.
> >>
> >>
> > And why not?
> >
> > genbox -cp protein.gro -cs sphere.gro
> >
> > should do exactly what you want, provided the sphere is large enough for
> > the protein.
> >
> > -Justin
> >
> >
> > Is there another feasible route to get to my desired configuration of
> the
> >> system ?
> >>
> >> Thanks in advance
> >>
> >>
> >> Best,
> >> SN
> >>
> >>
> >>
> >>
> > --
> > ========================================
> >
> > Justin A. Lemkul
> > Ph.D. Candidate
> > ICTAS Doctoral Scholar
> > MILES-IGERT Trainee
> > Department of Biochemistry
> > Virginia Tech
> > Blacksburg, VA
> > jalemkul[at]vt.edu | (540) 231-9080
> > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> >
> > ========================================
> > --
> > gmx-users mailing list gmx-users at gromacs.org
> > http://lists.gromacs.org/mailman/listinfo/gmx-users
> > Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> > Please don't post (un)subscribe requests to the list. Use the www
> interface
> > or send it to gmx-users-request at gromacs.org.
> > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
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> End of gmx-users Digest, Vol 85, Issue 61
> *****************************************
>
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