[gmx-users] Re: about PLP cofactor
pankaj at cdfd.org.in
pankaj at cdfd.org.in
Thu Jul 8 20:30:37 CEST 2004
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 .
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?
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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
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
------------------------------
Message: 9
Date: Thu, 8 Jul 2004 16:34:14 +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: <20040708162946.N6965-100000 at qt.dq.ufscar.br>
Content-Type: TEXT/PLAIN; charset=US-ASCII
Hi David,
indeed /usr/local is not on ld.so.conf, what should I do:
add it to this file or run all those scripts again?
about the nodes OS, it's just one dual box, so it's the same
OS for both processors.
thanks again,
andre'
/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/
Dr. Andre' Farias de Moura
Laboratorio de Quimica Teorica
Universidade Federal de Sao Carlos
Sao Carlos - SP - Brasil
/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/
On Thu, 8 Jul 2004, David wrote:
> 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
> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
>
> _______________________________________________
> 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.
>
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