[gmx-users] Re: about PLP cofactor
David
spoel at xray.bmc.uu.se
Thu Jul 8 21:41:26 CEST 2004
On Thu, 2004-07-08 at 20:30, pankaj at cdfd.org.in wrote:
> Hello all
> i used the dandee PRODRUG Server for topology of cofactor PLP.
> the i edit the topology file. but i donot know how i will connect the cofactor
> with one of the amino acid residue in protein (lysine).
> In receptor there is covalent bonding .
cp the specbond.dat file to your working directory and add your special
bond. then rerun pdb2gmx
> please help me
>
> thanks a lot
>
> pankaj kumar
> C/O Dr H.A.Najarajaram
> laboratory of computational biology and Bioinformatics
> center for dna fingerprinting and diagonistic
> nacharam,hyderabad,india
> ph.no 91-9848592448
>
>
>
> ---------REPLY TO-------------
> Date:Fri Jul 09 03:16:59 CST 2004
> FROM: gmx-users-request at gromacs.org
> To: gmx-users at gromacs.org
> Subject: gmx-users Digest, Vol 3, Issue 17
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> Today's Topics:
>
> 1. Sample Molecules Containing Silicon (Gromacs Newbie)
> 2. Re: g_sas, VdW radii (David)
> 3. Re: Help ! Some molecules go away from my bilayer..... (David)
> 4. Re: cannot compile parallel version (Andre Farias de Moura)
> 5. Linux binaries (Amy Petrik)
> 6. Re: simulation with cofactor (Semen Esilevsky)
> 7. Re: Linux binaries (David)
> 8. Re: cannot compile parallel version (David)
> 9. Re: cannot compile parallel version (Andre Farias de Moura)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Thu, 8 Jul 2004 10:41:12 -0700 (PDT)
> From: Gromacs Newbie <gromacs_newbie at yahoo.com>
> Subject: [gmx-users] Sample Molecules Containing Silicon
> To: gmx-users at gromacs.org
> Message-ID: <20040708174112.72772.qmail at web53408.mail.yahoo.com>
> Content-Type: text/plain; charset=us-ascii
>
> Well right now I'm looking for anything that has
> silicon support working in gromacs. Thanks.
>
> -Gary
>
>
>
>
> On Tue, 2004-07-06 at 21:41, Gromacs Newbie wrote:
> > Hi All,
> >
> > I was wondering if anyone out there has a some
> sample molecules that
> > contain silicon that I can use as a reference. I am
> having
> > difficulties creating one from scratch. Thank you
> in advance.
> >
> Can you be more specific? Are you after bond lengths
> and angles?
> > -Gary
> >
> >
>
>
>
> __________________________________
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> ------------------------------
>
> Message: 2
> Date: Thu, 08 Jul 2004 19:58:47 +0200
> From: David <spoel at xray.bmc.uu.se>
> Subject: Re: [gmx-users] g_sas, VdW radii
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <1089309527.5101.2.camel at h176n2fls34o1123.telia.com>
> Content-Type: text/plain
>
> On Thu, 2004-07-08 at 18:26, Michael Brunsteiner wrote:
> > dear all,
> >
> > Just tried to calculate the solvent accessible surface
> > area for a structure including non-protein molecules.
> > (using an extended OPLSAA FF, all atoms, however, are some
> > OPLSAA type)
> >
> > g_sas says:
> > WARNING: could not find a Van der Waals radius for 728 atoms
> >
> > Does that mean
> > a) these atoms are not included in the calculation of the SASA, or
> > b) some default value is used for these atoms ?
> b) 0.14 nm (see src/gmxlib/atomprop.c)
>
>
> --
> David.
> ________________________________________________________________________
> David van der Spoel, PhD, Assoc. 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: Thu, 08 Jul 2004 20:01:00 +0200
> From: David <spoel at xray.bmc.uu.se>
> Subject: Re: [gmx-users] Help ! Some molecules go away from my
> bilayer.....
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <1089309660.5102.4.camel at h176n2fls34o1123.telia.com>
> Content-Type: text/plain
>
> On Thu, 2004-07-08 at 18:36, sgaray at fbcb.unl.edu.ar wrote:
> > 6)MD without restriction (300K, 4ns, pressure
> > coupling: Berendsen, tao_p: 4ps, surface-
> > tension: cte). Again, one or two stearic acid go
> > away from the bilayer.
> > 7)MD without restriction (300K, 4ns, V cte.).
> > Again, one or two stearic acid go away from the
> > bilayer.
> >
> > Is it OK? The stearic's heads are very small, so Is it logical that
> > some of them are taken off the membrane due to the water
> > interactions? Any suggestion?
>
> What is the solubility of these beasts? Do they have long aliphatic
> tails?
> >
> >
> > Sergio Garay
> > Biochemist
> > Faculty of Biochemistry and Biological Science
> > Universidad Nacional del Litoral
> > Santa Fe (3000). Argentina
> >
> > _______________________________________________
> > 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, Assoc. 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: 4
> Date: Thu, 8 Jul 2004 15:38:17 +0000 (GMT)
> From: Andre Farias de Moura <andre at qt.dq.ufscar.br>
> Subject: Re: [gmx-users] cannot compile parallel version
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <20040708152227.N6965-100000 at qt.dq.ufscar.br>
> Content-Type: TEXT/PLAIN; charset=US-ASCII
>
>
> dear Oliver,
>
> I have tried your scripts with minor changes, as follows:
>
> (1) script to install lam-mpi latest version:
>
> export LAM_D=/usr/local/lam/;
> export FFTW_D=/usr/local/fftw/;
>
> tar -jxvf lam-7.0.6.tar.bz2
> cd lam-7.0.6
> ./configure --prefix=${LAM_D} --with-tcp-short=524288 --with-rpi=usysv
> --with-rsh=ssh
> make
> make install
>
>
> (2) script to install fftw:
>
> wget --passive ftp://ftp.fftw.org/pub/fftw/fftw-2.1.5.tar.gz
> tar -zxvf fftw-2.1.5.tar.gz
> cd fftw-2.1.5
>
> export LAM_D=/usr/local/lam/;
> export FFTW_D=/usr/local/fftw/;
> export PATH=${LAM_D}/bin:${PATH} # so mpicc gets found
>
> CPPFLAGS="-I${LAM_D}/include" \
> LDFLAGS="-L${LAM_D}/lib" \
> ./configure --prefix=${FFTW_D} --enable-type-prefix --enable-mpi
> make
> make install
>
>
> (3) script ot install mdrun parallel version:
>
> export LAM_D=/usr/local/lam/;
> export FFTW_D=/usr/local/fftw/;
>
> CPPFLAGS="-I${LAM_D}/include -I${FFTW_D}/include" \
> LDFLAGS="-L${LAM_D}/lib -L${FFTW_D}/lib" \
> ./configure --prefix=/opt/gromacs/3.2.1 --without-x \
> --enable-mpi --program-suffix=_mpi
> make mdrun
> make install-mdrun
>
> after half an hour running these script I ran mdrun parallel
> version as follows:
>
> grompp -f bpcdi -c bpcdi -p bpcdi -po out -o bpcdi -np 2
> mpirun -np 2 mdrun_mpi -s bpcdi -o bpcdi -c out -e out -g out -x bpcdi
> -v
> -np 2
>
> then I got these error messages:
>
> mdrun_mpi: relocation error: /usr/local/lib/libsfftw_mpi.so.2: symbol
> errno, version GLIBC_2.0 not defined in file libc.so.6 with link time
> reference
> mdrun_mpi: relocation error: /usr/local/lib/libsfftw_mpi.so.2: symbol
> errno, version GLIBC_2.0 not defined in file libc.so.6 with link time
> reference
> -----------------------------------------------------------------------------
> It seems that [at least] one of the processes that was started with
> mpirun did not invoke MPI_INIT before quitting (it is possible that
> more than one process did not invoke MPI_INIT -- mpirun was only
> notified of the first one, which was on node n0).
>
> mpirun can *only* be used with MPI programs (i.e., programs that
> invoke MPI_INIT and MPI_FINALIZE). You can use the "lamexec" program
> to run non-MPI programs over the lambooted nodes.
> -----------------------------------------------------------------------------
>
> I'm not pretty sure tha there was no error message at all during
> the installation procedure described above, due to the huge amount
> of output these scripts generated, but certainly the last message
> I got from them was something like: installation is ok, go on.
>
> can you figure out any reason why it is not working?
>
> the strangest thing about it is that it worked previously on the
> same machine running the same OS and using the default procedure
> described in the gromacs homepage.
>
> thank you in advance for any further suggestion.
>
> andre'
>
>
> /-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/
> Dr. Andre' Farias de Moura
> Laboratorio de Quimica Teorica
> Universidade Federal de Sao Carlos
> Sao Carlos - SP - Brasil
> /-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/
>
>
>
>
> ------------------------------
>
> Message: 5
> Date: Thu, 08 Jul 2004 14:24:15 -0400
> From: "Amy Petrik" <apetrik at umd.edu>
> Subject: [gmx-users] Linux binaries
> To: gmx-users at gromacs.org
> Message-ID: <1089311055.8f344320apetrik at umd.edu>
> Content-Type: text/plain; charset="UTF-8"
>
> Hi All!
> Here's a very beginner's question:
> I have downloaded the binaries for linux and they are in my usr/local directory.
> I have no idea what to do next. I used the gzip command to unzip the files
> but i don't think that the gromacs installation tree was set up. This is
> probably silly but what do I do next?? Thanks!
> Amy
>
>
>
> ------------------------------
>
> Message: 6
> Date: Thu, 8 Jul 2004 11:39:15 -0700 (PDT)
> From: Semen Esilevsky <yesint4 at yahoo.com>
> Subject: Re: [gmx-users] simulation with cofactor
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <20040708183915.82494.qmail at web40509.mail.yahoo.com>
> Content-Type: text/plain; charset=us-ascii
>
> > Hi every body
> > I am facing some problem when i m doing the
> > simulation of protein with
> > PLP cofactor. The initial pdb file has connect
> > records for plp with protein=
> > But during the simulation PLP is coming out of the
> > protein.
> > Is this because the PLP-Protein connection is not
> > defined in gromacs forcefeilds?
> > How can this be corrected?
>
> In order to simulate the protein with some cofactor in
> it you must have a topology for this thing. How did
> you build the topology of your codactor? What
> forcefield do you use?
>
>
>
> __________________________________
> Do you Yahoo!?
> Read only the mail you want - Yahoo! Mail SpamGuard.
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>
> ------------------------------
>
> Message: 7
> Date: Thu, 08 Jul 2004 20:55:58 +0200
> From: David <spoel at xray.bmc.uu.se>
> Subject: Re: [gmx-users] Linux binaries
> To: apetrik at umd.edu, Discussion list for GROMACS users
> <gmx-users at gromacs.org>
> Message-ID: <1089312958.5101.7.camel at h176n2fls34o1123.telia.com>
> Content-Type: text/plain
>
> On Thu, 2004-07-08 at 20:24, Amy Petrik wrote:
> > Hi All!
> > Here's a very beginner's question:
> > I have downloaded the binaries for linux and they are in my usr/local
> directory. I have no idea what to do next. I used the gzip command to unzip
> the files but i don't think that the gromacs installation tree was set
> up. This is probably silly but what do I do next?? Thanks!
> If you have installed RPMs without problem, you are ready to start the
> tutorial. Otherwise you will have to start by installing the software
> according to these instructions:
> http://www.gromacs.org/installation/index.php
> > Amy
> >
> > _______________________________________________
> > 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, Assoc. 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: 8
> Date: Thu, 08 Jul 2004 20:58:48 +0200
> From: David <spoel at xray.bmc.uu.se>
> Subject: Re: [gmx-users] cannot compile parallel version
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <1089313128.5101.10.camel at h176n2fls34o1123.telia.com>
> Content-Type: text/plain
>
> On Thu, 2004-07-08 at 17:38, Andre Farias de Moura wrote:
> > dear Oliver,
> >
> > I have tried your scripts with minor changes, as follows:
> >
> > (1) script to install lam-mpi latest version:
> >
> > export LAM_D=/usr/local/lam/;
> > export FFTW_D=/usr/local/fftw/;
> >
> > tar -jxvf lam-7.0.6.tar.bz2
> > cd lam-7.0.6
> > ./configure --prefix=${LAM_D} --with-tcp-short=524288 --with-rpi=usysv
> > --with-rsh=ssh
> > make
> > make install
> >
> >
> > (2) script to install fftw:
> >
> > wget --passive ftp://ftp.fftw.org/pub/fftw/fftw-2.1.5.tar.gz
> > tar -zxvf fftw-2.1.5.tar.gz
> > cd fftw-2.1.5
> >
> > export LAM_D=/usr/local/lam/;
> > export FFTW_D=/usr/local/fftw/;
> > export PATH=${LAM_D}/bin:${PATH} # so mpicc gets found
> >
> > CPPFLAGS="-I${LAM_D}/include" \
> > LDFLAGS="-L${LAM_D}/lib" \
> > ./configure --prefix=${FFTW_D} --enable-type-prefix --enable-mpi
> > make
> > make install
> >
> >
> > (3) script ot install mdrun parallel version:
> >
> > export LAM_D=/usr/local/lam/;
> > export FFTW_D=/usr/local/fftw/;
> >
> > CPPFLAGS="-I${LAM_D}/include -I${FFTW_D}/include" \
> > LDFLAGS="-L${LAM_D}/lib -L${FFTW_D}/lib" \
> > ./configure --prefix=/opt/gromacs/3.2.1 --without-x \
> > --enable-mpi --program-suffix=_mpi
> > make mdrun
> > make install-mdrun
> >
> > after half an hour running these script I ran mdrun parallel
> > version as follows:
> >
> > grompp -f bpcdi -c bpcdi -p bpcdi -po out -o bpcdi -np 2
> > mpirun -np 2 mdrun_mpi -s bpcdi -o bpcdi -c out -e out -g out -x bpcdi
> -v
> > -np 2
> >
> > then I got these error messages:
> >
> > mdrun_mpi: relocation error: /usr/local/lib/libsfftw_mpi.so.2: symbol
> > errno, version GLIBC_2.0 not defined in file libc.so.6 with link time
> > reference
> > mdrun_mpi: relocation error: /usr/local/lib/libsfftw_mpi.so.2: symbol
> > errno, version GLIBC_2.0 not defined in file libc.so.6 with link time
> > reference
>
> Are you sure that the /usr/local is available to all processors?
> If so, is /usr/local in the library search path (check /etc/ld.so.conf)
>
> Do you have different linux versions on the different nodes?
--
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. 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
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