Re: [gmx-users] Fwd: installing Gromacs4.6.3 on cygwin

[shahid nayeem]

Thanks Mark

$ make
[  0%] Built target gmxfftw
make[2]: *** No rule to make target
`//cygdrive/c/packages/gromacs-4.6.3/build/src/contrib/fftw/gmxfftw-prefix/lib/libfftw3.a',
needed by `src/gmxlib/cyggmx_d-8.dll'.  Stop.
CMakeFiles/Makefile2:1238: recipe for target
`src/gmxlib/CMakeFiles/gmx.dir/all' failed
make[1]: *** [src/gmxlib/CMakeFiles/gmx.dir/all] Error 2
Makefile:146: recipe for target `all' failed
make: *** [all] Error 2

I checked in folder
/cygdrive/c/packages/gromacs-4.6.3/build/src/contrib/fftw/gmxfftw-prefix/lib/libfftw3.a
, this file exists but perhaps `src/gmxlib/cyggmx_d-8.dll' is not able to
locate it.
Please help me

shahid Nayeem


On Wed, Sep 11, 2013 at 1:02 PM, shahid nayeem  wrote:

> Thanks. But when I ran make again I am getting this error
> [  0%] Built target gmxfftw
> make[2]: *** No rule to make target
> `//cygdrive/c/packages/gromacs-4.6.3/build/src/contrib/fftw/gmxfftw-prefix/lib/libfftw3.a',
> needed by `src/gmxlib/cyggmx_d-8.dll'.  Stop.
> CMakeFiles/Makefile2:1238: recipe for target
> `src/gmxlib/CMakeFiles/gmx.dir/all' failed
> make[1]: *** [src/gmxlib/CMakeFiles/gmx.dir/all] Error 2
> Makefile:146: recipe for target `all' failed
> make: *** [all] Error 2
>  shahid Nayeem
>
>
> On Wed, Sep 11, 2013 at 12:39 PM, Mark Abraham 
> wrote:
>
>> For technical reasons, parallel make with GMX_BUILD_OWN_FFTW can have
>> this problem. Run make a second time and it will work.
>>
>> Mark
>>
>> On Wed, Sep 11, 2013 at 6:22 AM, shahid nayeem 
>> wrote:
>> > Thanks Wahab
>> > I followed your instruction and added  #define HAVE_SYS_TIME_H
>> >
>> > at the very top of the file gmxlib/thread_mpi/impl.h.
>> > Then again in make command I got following errors.
>> > [ 53%] Building C object
>> >
>> src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_avx_256_double/nb_kernel_ElecRF_VdwCSTab_GeomP1P1_avx_256_double.c.o
>> > [ 53%] Building C object
>> >
>> src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_avx_256_double/nb_kernel_ElecRF_VdwCSTab_GeomW3P1_avx_256_double.c.o
>> > [ 53%] Building C object
>> >
>> src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_avx_256_double/nb_kernel_ElecRF_VdwCSTab_GeomW3W3_avx_256_double.c.o
>> > [ 53%] Building C object
>> >
>> src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_avx_256_double/nb_kernel_ElecRF_VdwCSTab_GeomW4P1_avx_256_double.c.o
>> > [ 53%] Building C object
>> >
>> src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_avx_256_double/nb_kernel_ElecRF_VdwCSTab_GeomW4W4_avx_256_double.c.o
>> > [ 55%] Building C object
>> >
>> src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_avx_256_double/nb_kernel_ElecRF_VdwLJ_GeomP1P1_avx_256_double.c.o
>> > [ 55%] Building C object
>> >
>> src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_avx_256_double/nb_kernel_ElecRF_VdwLJ_GeomW3P1_avx_256_double.c.o
>> > [ 55%] Building C object
>> >
>> src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_avx_256_double/nb_kernel_ElecRF_VdwLJ_GeomW3W3_avx_256_double.c.o
>> > [ 55%] Building C object
>> >
>> src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_avx_256_double/nb_kernel_ElecRF_VdwLJ_GeomW4P1_avx_256_double.c.o
>> > [ 55%] Building C object
>> >
>> src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_avx_256_double/nb_kernel_ElecRF_VdwLJ_GeomW4W4_avx_256_double.c.o
>> > [ 55%] Building C object
>> >
>> src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_avx_256_double/nb_kernel_ElecRF_VdwNone_GeomP1P1_avx_256_double.c.o
>> > [ 55%] Building C object
>> >
>> src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_avx_256_double/nb_kernel_ElecRF_VdwNone_GeomW3P1_avx_256_double.c.o
>> > [ 55%] Building C object
>> >
>> src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_avx_256_double/nb_kernel_ElecRF_VdwNone_GeomW3W3_avx_256_double.c.o
>> > [ 56%] Building C object
>> >
>> src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_avx_256_double/nb_kernel_ElecRF_VdwNone_GeomW4P1_avx_256_double.c.o
>> > [ 56%] Building C object
>> >
>> src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_avx_256_double/nb_kernel_ElecRF_VdwNone_GeomW4W4_avx_256_double.c.o
>> > make[2]: *** No rule to make target
>> >
>> `//cygdrive/c/packages/gromacs-4.6.3/build/src/contrib/fftw/gmxfftw-prefix/lib/libfftw3.a',
>> > needed by `src/gmxlib/cyggmx_d-8.dll'.  Stop.
>> > CMakeFiles/Makefile2:1238: recipe for target
>> > `src/gmxlib/CMakeFiles/gmx.dir/all' failed
>> > make[1]: *** [src/gmxlib/CMakeFiles/gmx.di

Re: [gmx-users] Fwd: installing Gromacs4.6.3 on cygwin

[shahid nayeem]

Thanks. But when I ran make again I am getting this error
[  0%] Built target gmxfftw
make[2]: *** No rule to make target
`//cygdrive/c/packages/gromacs-4.6.3/build/src/contrib/fftw/gmxfftw-prefix/lib/libfftw3.a',
needed by `src/gmxlib/cyggmx_d-8.dll'.  Stop.
CMakeFiles/Makefile2:1238: recipe for target
`src/gmxlib/CMakeFiles/gmx.dir/all' failed
make[1]: *** [src/gmxlib/CMakeFiles/gmx.dir/all] Error 2
Makefile:146: recipe for target `all' failed
make: *** [all] Error 2
 shahid Nayeem


On Wed, Sep 11, 2013 at 12:39 PM, Mark Abraham wrote:

> For technical reasons, parallel make with GMX_BUILD_OWN_FFTW can have
> this problem. Run make a second time and it will work.
>
> Mark
>
> On Wed, Sep 11, 2013 at 6:22 AM, shahid nayeem  wrote:
> > Thanks Wahab
> > I followed your instruction and added  #define HAVE_SYS_TIME_H
> >
> > at the very top of the file gmxlib/thread_mpi/impl.h.
> > Then again in make command I got following errors.
> > [ 53%] Building C object
> >
> src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_avx_256_double/nb_kernel_ElecRF_VdwCSTab_GeomP1P1_avx_256_double.c.o
> > [ 53%] Building C object
> >
> src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_avx_256_double/nb_kernel_ElecRF_VdwCSTab_GeomW3P1_avx_256_double.c.o
> > [ 53%] Building C object
> >
> src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_avx_256_double/nb_kernel_ElecRF_VdwCSTab_GeomW3W3_avx_256_double.c.o
> > [ 53%] Building C object
> >
> src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_avx_256_double/nb_kernel_ElecRF_VdwCSTab_GeomW4P1_avx_256_double.c.o
> > [ 53%] Building C object
> >
> src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_avx_256_double/nb_kernel_ElecRF_VdwCSTab_GeomW4W4_avx_256_double.c.o
> > [ 55%] Building C object
> >
> src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_avx_256_double/nb_kernel_ElecRF_VdwLJ_GeomP1P1_avx_256_double.c.o
> > [ 55%] Building C object
> >
> src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_avx_256_double/nb_kernel_ElecRF_VdwLJ_GeomW3P1_avx_256_double.c.o
> > [ 55%] Building C object
> >
> src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_avx_256_double/nb_kernel_ElecRF_VdwLJ_GeomW3W3_avx_256_double.c.o
> > [ 55%] Building C object
> >
> src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_avx_256_double/nb_kernel_ElecRF_VdwLJ_GeomW4P1_avx_256_double.c.o
> > [ 55%] Building C object
> >
> src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_avx_256_double/nb_kernel_ElecRF_VdwLJ_GeomW4W4_avx_256_double.c.o
> > [ 55%] Building C object
> >
> src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_avx_256_double/nb_kernel_ElecRF_VdwNone_GeomP1P1_avx_256_double.c.o
> > [ 55%] Building C object
> >
> src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_avx_256_double/nb_kernel_ElecRF_VdwNone_GeomW3P1_avx_256_double.c.o
> > [ 55%] Building C object
> >
> src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_avx_256_double/nb_kernel_ElecRF_VdwNone_GeomW3W3_avx_256_double.c.o
> > [ 56%] Building C object
> >
> src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_avx_256_double/nb_kernel_ElecRF_VdwNone_GeomW4P1_avx_256_double.c.o
> > [ 56%] Building C object
> >
> src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_avx_256_double/nb_kernel_ElecRF_VdwNone_GeomW4W4_avx_256_double.c.o
> > make[2]: *** No rule to make target
> >
> `//cygdrive/c/packages/gromacs-4.6.3/build/src/contrib/fftw/gmxfftw-prefix/lib/libfftw3.a',
> > needed by `src/gmxlib/cyggmx_d-8.dll'.  Stop.
> > CMakeFiles/Makefile2:1238: recipe for target
> > `src/gmxlib/CMakeFiles/gmx.dir/all' failed
> > make[1]: *** [src/gmxlib/CMakeFiles/gmx.dir/all] Error 2
> > Makefile:146: recipe for target `all' failed
> > make: *** [all] Error 2
> >
> > Please help me to compile gromacs 4.6.3 on cygwin
> >
> > Shahid Nayeem
> >
> >
> > On Tue, Sep 10, 2013 at 9:13 PM, Mirco Wahab <
> > mirco.wa...@chemie.tu-freiberg.de> wrote:
> >
> >> On 10.09.2013 08:20, shahid nayeem wrote:
> >>
> >>> I am installing gromacs -4.6.3 on cygwin with following commands
> >>> tar -xvzf gramcs-4.6.3.tar.gz
> >>> cd gromacs-4.6.3
> >>> mkdir build
> >>> cd build
> >>>   cmake .. -DGMX_BUILD_OWN_FFTW=ON -DGMX_DOUBLE=on
> >>> It runs fine and write file in build directory.
> >>> when I run make command it gives following error.
> >>> ...
> >>>
> >>> /cygdrive/c/packages/gromacs-**4.6.3/src/gmxlib/thread_mpi/**
> >>> impl.h:504:20:
> >>> error: field ‘timer_init’ has incomplete type
> >>

Re: [gmx-users] Fwd: installing Gromacs4.6.3 on cygwin

[shahid nayeem]

Thanks Wahab
I followed your instruction and added  #define HAVE_SYS_TIME_H

at the very top of the file gmxlib/thread_mpi/impl.h.
Then again in make command I got following errors.
[ 53%] Building C object
src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_avx_256_double/nb_kernel_ElecRF_VdwCSTab_GeomP1P1_avx_256_double.c.o
[ 53%] Building C object
src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_avx_256_double/nb_kernel_ElecRF_VdwCSTab_GeomW3P1_avx_256_double.c.o
[ 53%] Building C object
src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_avx_256_double/nb_kernel_ElecRF_VdwCSTab_GeomW3W3_avx_256_double.c.o
[ 53%] Building C object
src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_avx_256_double/nb_kernel_ElecRF_VdwCSTab_GeomW4P1_avx_256_double.c.o
[ 53%] Building C object
src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_avx_256_double/nb_kernel_ElecRF_VdwCSTab_GeomW4W4_avx_256_double.c.o
[ 55%] Building C object
src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_avx_256_double/nb_kernel_ElecRF_VdwLJ_GeomP1P1_avx_256_double.c.o
[ 55%] Building C object
src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_avx_256_double/nb_kernel_ElecRF_VdwLJ_GeomW3P1_avx_256_double.c.o
[ 55%] Building C object
src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_avx_256_double/nb_kernel_ElecRF_VdwLJ_GeomW3W3_avx_256_double.c.o
[ 55%] Building C object
src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_avx_256_double/nb_kernel_ElecRF_VdwLJ_GeomW4P1_avx_256_double.c.o
[ 55%] Building C object
src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_avx_256_double/nb_kernel_ElecRF_VdwLJ_GeomW4W4_avx_256_double.c.o
[ 55%] Building C object
src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_avx_256_double/nb_kernel_ElecRF_VdwNone_GeomP1P1_avx_256_double.c.o
[ 55%] Building C object
src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_avx_256_double/nb_kernel_ElecRF_VdwNone_GeomW3P1_avx_256_double.c.o
[ 55%] Building C object
src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_avx_256_double/nb_kernel_ElecRF_VdwNone_GeomW3W3_avx_256_double.c.o
[ 56%] Building C object
src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_avx_256_double/nb_kernel_ElecRF_VdwNone_GeomW4P1_avx_256_double.c.o
[ 56%] Building C object
src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_avx_256_double/nb_kernel_ElecRF_VdwNone_GeomW4W4_avx_256_double.c.o
make[2]: *** No rule to make target
`//cygdrive/c/packages/gromacs-4.6.3/build/src/contrib/fftw/gmxfftw-prefix/lib/libfftw3.a',
needed by `src/gmxlib/cyggmx_d-8.dll'.  Stop.
CMakeFiles/Makefile2:1238: recipe for target
`src/gmxlib/CMakeFiles/gmx.dir/all' failed
make[1]: *** [src/gmxlib/CMakeFiles/gmx.dir/all] Error 2
Makefile:146: recipe for target `all' failed
make: *** [all] Error 2

Please help me to compile gromacs 4.6.3 on cygwin

Shahid Nayeem


On Tue, Sep 10, 2013 at 9:13 PM, Mirco Wahab <
mirco.wa...@chemie.tu-freiberg.de> wrote:

> On 10.09.2013 08:20, shahid nayeem wrote:
>
>> I am installing gromacs -4.6.3 on cygwin with following commands
>> tar -xvzf gramcs-4.6.3.tar.gz
>> cd gromacs-4.6.3
>> mkdir build
>> cd build
>>   cmake .. -DGMX_BUILD_OWN_FFTW=ON -DGMX_DOUBLE=on
>> It runs fine and write file in build directory.
>> when I run make command it gives following error.
>> ...
>>
>> /cygdrive/c/packages/gromacs-**4.6.3/src/gmxlib/thread_mpi/**
>> impl.h:504:20:
>> error: field ‘timer_init’ has incomplete type
>>   struct timeval timer_init;
>>  ^
>> src/gmxlib/CMakeFiles/gmx.dir/**build.make:3070: recipe for target
>>
>
> The Gromacs-file "gmxlib/thread_mpi/impl.h" is missing the
> correct #define for the "unixish" Cygwin pseudo-os. You can
> add it by inserting
>
>  #define HAVE_SYS_TIME_H
>
> at the very top of the file gmxlib/thread_mpi/impl.h
>
> Then the package will probably compile and link, but
> mdrun's thread-mpi (tMPI) will not work on Cygwin
> (didn't work last time I tried).
>
> So you could do the following: 1) install the Gromacs
> package with "normal" compilation, and 2) build and
> install the openmpi-version of mdrun (mdrun_mpi).
>
> (1) cmake-options for package:
> ...
>   -DGMX_GPU=OFF \
>   -DGMX_PREFER_STATIC_LIBS=ON   \
> ...
>
> make -j4 install
>
> (delete all files from the build path)
>
> (2) cmake options for mdrun_mpi
> ...
>   -DGMX_GPU=OFF\
>   -DGMX_MPI=ON \
>   -DGMX_PREFER_STATIC_LIBS=ON  \
> ...
>
> make -j4 install-mdrun
>
> The openmpi-version (mdrun_mpi) runs reasonable on
> Cygwin/64 1.7.25, but not as fast as the native
> windows version (compiled with visual studio 10 or 12).
> The windows-compiled version of 4.6.3 is very robust and
> allows to link

[gmx-users] Fwd: installing Gromacs4.6.3 on cygwin

[shahid nayeem]

Dear all
I am installing gromacs -4.6.3 on cygwin with following commands
tar -xvzf gramcs-4.6.3.tar.gz
cd gromacs-4.6.3
mkdir build
cd build
 cmake .. -DGMX_BUILD_OWN_FFTW=ON -DGMX_DOUBLE=on
It runs fine and write file in build directory.
when I run make command it gives following error.

[ 15%] Building C object
src/gmxlib/CMakeFiles/gmx.dir/selection/sm_permute.c.o
[ 15%] Building C object
src/gmxlib/CMakeFiles/gmx.dir/selection/sm_position.c.o
[ 15%] Building C object src/gmxlib/CMakeFiles/gmx.dir/selection/sm_same.c.o
[ 15%] Building C object
src/gmxlib/CMakeFiles/gmx.dir/selection/sm_simple.c.o
[ 15%] Building C object src/gmxlib/CMakeFiles/gmx.dir/selection/symrec.c.o
[ 15%] Building C object
src/gmxlib/CMakeFiles/gmx.dir/trajana/centerofmass.c.o
[ 16%] Building C object
src/gmxlib/CMakeFiles/gmx.dir/trajana/displacement.c.o
[ 16%] Building C object src/gmxlib/CMakeFiles/gmx.dir/trajana/indexutil.c.o
[ 16%] Building C object src/gmxlib/CMakeFiles/gmx.dir/trajana/nbsearch.c.o
[ 16%] Building C object src/gmxlib/CMakeFiles/gmx.dir/trajana/poscalc.c.o
[ 16%] Building C object src/gmxlib/CMakeFiles/gmx.dir/trajana/position.c.o
[ 16%] Building C object src/gmxlib/CMakeFiles/gmx.dir/trajana/trajana.c.o
[ 16%] Building C object
src/gmxlib/CMakeFiles/gmx.dir/statistics/gmx_statistics.c.o
[ 16%] Building C object
src/gmxlib/CMakeFiles/gmx.dir/statistics/histogram.c.o
[ 16%] Building C object
src/gmxlib/CMakeFiles/gmx.dir/thread_mpi/errhandler.c.o
[ 17%] Building C object
src/gmxlib/CMakeFiles/gmx.dir/thread_mpi/tmpi_malloc.c.o
[ 17%] Building C object src/gmxlib/CMakeFiles/gmx.dir/thread_mpi/atomic.c.o
In file included from
/cygdrive/c/packages/gromacs-4.6.3/src/gmxlib/thread_mpi/atomic.c:38:0:
/cygdrive/c/packages/gromacs-4.6.3/src/gmxlib/thread_mpi/impl.h:504:20:
error: field ‘timer_init’ has incomplete type
 struct timeval timer_init;
^
src/gmxlib/CMakeFiles/gmx.dir/build.make:3070: recipe for target
`src/gmxlib/CMakeFiles/gmx.dir/thread_mpi/atomic.c.o' failed
make[2]: *** [src/gmxlib/CMakeFiles/gmx.dir/thread_mpi/atomic.c.o] Error 1
CMakeFiles/Makefile2:1238: recipe for target
`src/gmxlib/CMakeFiles/gmx.dir/all' failed
make[1]: *** [src/gmxlib/CMakeFiles/gmx.dir/all] Error 2
Makefile:146: recipe for target `all' failed
make: *** [all] Error 2
 Please help me to install this version of gromacs on cygwin

Shahid
--
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[gmx-users] installing Gromacs4.6.3 on cygwin

[shahid nayeem]

Dear all
I am installing gromacs -4.6.3 on cygwin with following commands
tar -xvzf gramcs-4.6.3.tar.gz
cd gromacs-4.6.3
mkdir build
cd build
 cmake .. -DGMX_BUILD_OWN_FFTW=ON -DGMX_DOUBLE=on
It runs fine and write file in build directory.
when I run make command it gives following error.

[ 15%] Building C object
src/gmxlib/CMakeFiles/gmx.dir/selection/sm_permute.c.o
[ 15%] Building C object
src/gmxlib/CMakeFiles/gmx.dir/selection/sm_position.c.o
[ 15%] Building C object src/gmxlib/CMakeFiles/gmx.dir/selection/sm_same.c.o
[ 15%] Building C object
src/gmxlib/CMakeFiles/gmx.dir/selection/sm_simple.c.o
[ 15%] Building C object src/gmxlib/CMakeFiles/gmx.dir/selection/symrec.c.o
[ 15%] Building C object
src/gmxlib/CMakeFiles/gmx.dir/trajana/centerofmass.c.o
[ 16%] Building C object
src/gmxlib/CMakeFiles/gmx.dir/trajana/displacement.c.o
[ 16%] Building C object src/gmxlib/CMakeFiles/gmx.dir/trajana/indexutil.c.o
[ 16%] Building C object src/gmxlib/CMakeFiles/gmx.dir/trajana/nbsearch.c.o
[ 16%] Building C object src/gmxlib/CMakeFiles/gmx.dir/trajana/poscalc.c.o
[ 16%] Building C object src/gmxlib/CMakeFiles/gmx.dir/trajana/position.c.o
[ 16%] Building C object src/gmxlib/CMakeFiles/gmx.dir/trajana/trajana.c.o
[ 16%] Building C object
src/gmxlib/CMakeFiles/gmx.dir/statistics/gmx_statistics.c.o
[ 16%] Building C object
src/gmxlib/CMakeFiles/gmx.dir/statistics/histogram.c.o
[ 16%] Building C object
src/gmxlib/CMakeFiles/gmx.dir/thread_mpi/errhandler.c.o
[ 17%] Building C object
src/gmxlib/CMakeFiles/gmx.dir/thread_mpi/tmpi_malloc.c.o
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 Please help me to install this version of gromacs on cygwin

Shahid
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Re: [gmx-users] constant protonation state MD

[shahid nayeem]

It is a peptide.
Shahid


On Mon, May 6, 2013 at 4:46 AM, Jesper Sørensen  wrote:

> Shahid,
>
> This must be system dependent then because there are experimental methods,
> e.g. NMR and CD, that can help determine the secondary structure of
> proteins/peptides are various pH ranges.
> What is your system? A peptide? A globular protein?
>
> Best,
> Jesper
>
> On May 3, 2013, at 7:33 PM, shahid nayeem  wrote:
>
> > Thanks a lot Erik and Baptista
> > I am interested in simulating the change in secondary structure which is
> > supposed to be influenced by the change in the pH environment of the
> cell.
> > Experimentally it is not known but it has been proposed by many that the
> > change in pH leads to change in conformation. I did constant protonation
> > state MD at two different pH. I got an alpha helix converting to beta
> sheet
> > at higher pH but not at lower pH. I am bothered to prove the reliability
> of
> > the simulation results as experimentally it cant be established.
> >
> > Shahid
> >
> >
> > On Sat, May 4, 2013 at 5:46 AM,  wrote:
> >
> >> Hi Shahid,
> >>
> >> As Erik said, it depends... on your system, on the process you are
> >> studying in that system, on the property you think it's relevant to
> study
> >> that process, etc.
> >>
> >> If your question refers to the (de)protonation of acidic and basic
> groups
> >> usually occuring in aqueous solution, there are methods to perform what
> is
> >> called constant-pH MD, where the protonation states of those groups
> change
> >> in a discrete or continuous way along the simulation. If you are
> >> interested, start with the corresponding GROMACS how-to (
> >> http://www.gromacs.org/**Documentation/How-tos/**Constant_pH_Simulation
> <http://www.gromacs.org/Documentation/How-tos/Constant_pH_Simulation>)
> >> and then search the literature.
> >>
> >> In any case, you don't need any of that fancy stuff unless you have
> >> reasons to think that the properties you want to study in your system
> are
> >> strongly dependent on protonation-conformation coupling effects. In some
> >> cases you may be suspicious about the effect of the protonation state of
> >> one group (e.g., a histidine), but that can be simply tested by
> performing
> >> two constant-protonation MD simulations, one for each state (you can
> even
> >> try to use a linear response approximation on top of that). But in most
> >> cases you don't need even that.
> >>
> >> For what it's worth: I was one of the first to develop and apply
> >> constant-pH MD and I don't bother to use it most of the time... :)
> >>
> >> Best,
> >> Antonio
> >>
> >>
> >> On Fri, 3 May 2013, Erik Marklund wrote:
> >>
> >> Yes that's what lambda dynamics does. I mentioned it since it addresses
> >>> the interplay between protonation and structure. So to answer your
> original
> >>> question: it depends.
> >>>
> >>> Erik
> >>>
> >>> On 3 May 2013, at 15:27, shahid nayeem  wrote:
> >>>
> >>> If I know correctly in lambda dynamics the dynamics of
> >>>> protonation/deprotonation equilibria is accounted for while my
> question
> >>>> relates to the typical constant protonation MD where each titratable
> >>>> group
> >>>> remains in one protonation state throughout the simulation. Please
> >>>> educate
> >>>> me
> >>>> Shahid
> >>>>
> >>>>
> >>>> On Fri, May 3, 2013 at 6:22 PM, Erik Marklund 
> >>>> wrote:
> >>>>
> >>>> I don't have one in mind. It's a delicate question and perhaps I
> >>>>> shouldn't
> >>>>> have phrased it the way I did. Nevertheless, the pKa of most side
> chains
> >>>>> mean that their protonation will be dominated by one state for most
> pH
> >>>>> values. pKa-shifts and complicated interplay between protonation and
> >>>>> structure cause exceptions to this and you should be aware that such
> >>>>> things
> >>>>> may in some cases be important. Also consider the timescales of
> >>>>> pH-depedent
> >>>>> structural changes and the length of your simulations. You could
> check
> >>>>> out
> >>>>> 

Re: [gmx-users] constant protonation state MD

[shahid nayeem]

Thanks a lot Erik and Baptista
I am interested in simulating the change in secondary structure which is
supposed to be influenced by the change in the pH environment of the cell.
Experimentally it is not known but it has been proposed by many that the
change in pH leads to change in conformation. I did constant protonation
state MD at two different pH. I got an alpha helix converting to beta sheet
at higher pH but not at lower pH. I am bothered to prove the reliability of
the simulation results as experimentally it cant be established.

Shahid


On Sat, May 4, 2013 at 5:46 AM,  wrote:

> Hi Shahid,
>
> As Erik said, it depends... on your system, on the process you are
> studying in that system, on the property you think it's relevant to study
> that process, etc.
>
> If your question refers to the (de)protonation of acidic and basic groups
> usually occuring in aqueous solution, there are methods to perform what is
> called constant-pH MD, where the protonation states of those groups change
> in a discrete or continuous way along the simulation. If you are
> interested, start with the corresponding GROMACS how-to (
> http://www.gromacs.org/**Documentation/How-tos/**Constant_pH_Simulation<http://www.gromacs.org/Documentation/How-tos/Constant_pH_Simulation>)
> and then search the literature.
>
> In any case, you don't need any of that fancy stuff unless you have
> reasons to think that the properties you want to study in your system are
> strongly dependent on protonation-conformation coupling effects. In some
> cases you may be suspicious about the effect of the protonation state of
> one group (e.g., a histidine), but that can be simply tested by performing
> two constant-protonation MD simulations, one for each state (you can even
> try to use a linear response approximation on top of that). But in most
> cases you don't need even that.
>
> For what it's worth: I was one of the first to develop and apply
> constant-pH MD and I don't bother to use it most of the time... :)
>
> Best,
> Antonio
>
>
> On Fri, 3 May 2013, Erik Marklund wrote:
>
>  Yes that's what lambda dynamics does. I mentioned it since it addresses
>> the interplay between protonation and structure. So to answer your original
>> question: it depends.
>>
>> Erik
>>
>> On 3 May 2013, at 15:27, shahid nayeem  wrote:
>>
>>  If I know correctly in lambda dynamics the dynamics of
>>> protonation/deprotonation equilibria is accounted for while my question
>>> relates to the typical constant protonation MD where each titratable
>>> group
>>> remains in one protonation state throughout the simulation. Please
>>> educate
>>> me
>>> Shahid
>>>
>>>
>>> On Fri, May 3, 2013 at 6:22 PM, Erik Marklund 
>>> wrote:
>>>
>>>  I don't have one in mind. It's a delicate question and perhaps I
>>>> shouldn't
>>>> have phrased it the way I did. Nevertheless, the pKa of most side chains
>>>> mean that their protonation will be dominated by one state for most pH
>>>> values. pKa-shifts and complicated interplay between protonation and
>>>> structure cause exceptions to this and you should be aware that such
>>>> things
>>>> may in some cases be important. Also consider the timescales of
>>>> pH-depedent
>>>> structural changes and the length of your simulations. You could check
>>>> out
>>>> the papers on lambda dynamics by C. Brooks III for an interesting take
>>>> on
>>>> sampling multiple protonation states.
>>>>
>>>> Best,
>>>>
>>>> Erik
>>>>
>>>> On 3 May 2013, at 14:05, shahid nayeem  wrote:
>>>>
>>>>  Thanks a lot Erik. Could I get some reference based on which you say
>>>>> that
>>>>> much of the structural biology will be largely unaffected.
>>>>>
>>>>> Shahid
>>>>>
>>>>>
>>>>> On Fri, May 3, 2013 at 1:05 PM, Erik Marklund 
>>>>>
>>>> wrote:
>>>>
>>>>>
>>>>>  There's no general answer to that. Proton conductivity measurements,
>>>>>> for
>>>>>> instance, will be horribly wrong without dynamic protonation. Much
>>>>>> (but
>>>>>>
>>>>> not
>>>>
>>>>> all) structural biology, however, will be largely unaffected.
>>>>>>
>>>>>> Erik
>>>>>>
>>>>>>

Re: [gmx-users] constant protonation state MD

[shahid nayeem]

If I know correctly in lambda dynamics the dynamics of
protonation/deprotonation equilibria is accounted for while my question
relates to the typical constant protonation MD where each titratable group
remains in one protonation state throughout the simulation. Please educate
me
Shahid


On Fri, May 3, 2013 at 6:22 PM, Erik Marklund  wrote:

> I don't have one in mind. It's a delicate question and perhaps I shouldn't
> have phrased it the way I did. Nevertheless, the pKa of most side chains
> mean that their protonation will be dominated by one state for most pH
> values. pKa-shifts and complicated interplay between protonation and
> structure cause exceptions to this and you should be aware that such things
> may in some cases be important. Also consider the timescales of pH-depedent
> structural changes and the length of your simulations. You could check out
> the papers on lambda dynamics by C. Brooks III for an interesting take on
> sampling multiple protonation states.
>
> Best,
>
> Erik
>
> On 3 May 2013, at 14:05, shahid nayeem  wrote:
>
> > Thanks a lot Erik. Could I get some reference based on which you say that
> > much of the structural biology will be largely unaffected.
> >
> > Shahid
> >
> >
> > On Fri, May 3, 2013 at 1:05 PM, Erik Marklund 
> wrote:
> >
> >> There's no general answer to that. Proton conductivity measurements, for
> >> instance, will be horribly wrong without dynamic protonation. Much (but
> not
> >> all) structural biology, however, will be largely unaffected.
> >>
> >> Erik
> >>
> >> On 3 May 2013, at 04:30, shahid nayeem  wrote:
> >>
> >>> Dear all
> >>>
> >>> Can someone enlighten me on the reliability of the results obtained
> from
> >>> constant protonation state (assigned by different pKa value at
> different
> >>> pH) MD simulation. Also want to know its reliability in case of
> implicit
> >>> solvation model such as PB/GB calculation.
> >>>
> >>> Shahid
> >>> --
> >>> gmx-users mailing listgmx-users@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-requ...@gromacs.org.
> >>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >>
> >> --
> >> gmx-users mailing listgmx-users@gromacs.org
> >> http://lists.gromacs.org/mailman/listinfo/gmx-users
> >> * Please search the archive at
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> >>
> > --
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Re: [gmx-users] constant protonation state MD

[shahid nayeem]

Thanks a lot Erik. Could I get some reference based on which you say that
much of the structural biology will be largely unaffected.

Shahid


On Fri, May 3, 2013 at 1:05 PM, Erik Marklund  wrote:

> There's no general answer to that. Proton conductivity measurements, for
> instance, will be horribly wrong without dynamic protonation. Much (but not
> all) structural biology, however, will be largely unaffected.
>
> Erik
>
> On 3 May 2013, at 04:30, shahid nayeem  wrote:
>
> > Dear all
> >
> > Can someone enlighten me on the reliability of the results obtained from
> > constant protonation state (assigned by different pKa value at different
> > pH) MD simulation. Also want to know its reliability in case of implicit
> > solvation model such as PB/GB calculation.
> >
> > Shahid
> > --
> > gmx-users mailing listgmx-users@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-requ...@gromacs.org.
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> --
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[gmx-users] constant protonation state MD

[shahid nayeem]

Dear all

Can someone enlighten me on the reliability of the results obtained from
constant protonation state (assigned by different pKa value at different
pH) MD simulation. Also want to know its reliability in case of implicit
solvation model such as PB/GB calculation.

Shahid
-- 
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Re: [gmx-users] .top file from .tpr and .xtc

[shahid nayeem]

I did it. Simply I changed the name of Cys which forms interchain
dsiulfide bond to CYS2 in the separated pdb file and I used G43a1
forcefeild to run pdb2gmx. This gives a topology with same number of
atom which is present in .xtc file. CYS2 is present .rtp file of G43a1
forcefeild probably to form interchain disulfide bond reading from
specbond.dat. Am I right in generating such half disulfide bond
topology.
shahid

On Tue, Mar 19, 2013 at 2:10 PM, francesco oteri
 wrote:
> Could you simply edit the file and removing the atom from [atoms] section ?
> grompp wil complain regarding the line containing interactions. But also
> these
> few lines can be removed. Otherwise, vmd has the TopoTools that write the
> .top
> topology of the loaded pdb. Unfortunately, this topologyes are not useful
> for carrying
> out MD because they lack parameters. In any case are good for analysis!
>
> Francesco
>
>
> 2013/3/19 shahid nayeem 
>
>> Thanks Francesco.
>> But my problem is exactly opposite. I do have a .top file containing
>> both chain linked by disulfide bridge. I ran the simulation. Now I
>> have extracted .xtc file for each chain separately and I want the
>> corresponding, separate .top file for each chain. when I separate the
>> pdb and run the pdb2gmx I get one hydrogen on SG atom of Cys which is
>> absent in .xtc file. So the .top file generated this way has one atom
>> more as compared to .xtc file.
>> shahid
>>
>> On Tue, Mar 19, 2013 at 1:07 PM, francesco oteri
>>  wrote:
>> > Hi,
>> > if you were able to obtain a simulation it means you had a valid .top
>> file!
>> > In any case, gromacs recognises disulfide basing on the distance beween
>> the
>> > SG atoms.
>> > In addition, the two chains are supposed to be in the same molecule.
>> > So, my advice is, remove all the TER from pdb (but the last one), leave
>> the
>> > chain id and use pdb2gmx
>> > with the option -chainsep ter. The result is supposed to be a topology
>> > where your chain are grouped in
>> > a single molecule,making possible to create the bridge, and at the same
>> > time you keep the chain name
>> > for future analysis.
>> >
>> > Francesco
>> >
>> >
>> > 2013/3/19 shahid nayeem 
>> >
>> >> Hi
>> >> To be more clear I have .xtc file for a disulfide linked complex of
>> >> two chains. From this trajectory I can extract .xtc file for
>> >> individual chains. But when I generate .top file from individual chain
>> >> pdb I get one atom extra in .top file i.e. protonated SG of Cys which
>> >> I dont need in order to make my .xtc and .top file compatible.
>> >> Shahid
>> >>
>> >> On Tue, Mar 19, 2013 at 2:07 AM, Justin Lemkul  wrote:
>> >> >
>> >> >
>> >> > On 3/18/13 12:35 PM, shahid nayeem wrote:
>> >> >>
>> >> >> Hi
>> >> >> Is it possible to write .top file from .xtc and .tpr using index.ndx
>> >> >> so that .top is available for tailormade components of simulated
>> >> >> protein.
>> >> >>
>> >> >
>> >> > All topology information is in the .tpr, but not in .top format.  You
>> >> may be
>> >> > able to post-process the output of gmxdump to produce some hacked
>> >> version,
>> >> > but that's just a bit of a hand-waving guess.  I don't really
>> understand
>> >> > what your objective is.
>> >> >
>> >> > -Justin
>> >> >
>> >> > --
>> >> > 
>> >> >
>> >> > Justin A. Lemkul, Ph.D.
>> >> > Research Scientist
>> >> > 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 listgmx-users@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-requ...

Re: [gmx-users] .top file from .tpr and .xtc

[shahid nayeem]

Thanks Francesco.
But my problem is exactly opposite. I do have a .top file containing
both chain linked by disulfide bridge. I ran the simulation. Now I
have extracted .xtc file for each chain separately and I want the
corresponding, separate .top file for each chain. when I separate the
pdb and run the pdb2gmx I get one hydrogen on SG atom of Cys which is
absent in .xtc file. So the .top file generated this way has one atom
more as compared to .xtc file.
shahid

On Tue, Mar 19, 2013 at 1:07 PM, francesco oteri
 wrote:
> Hi,
> if you were able to obtain a simulation it means you had a valid .top file!
> In any case, gromacs recognises disulfide basing on the distance beween the
> SG atoms.
> In addition, the two chains are supposed to be in the same molecule.
> So, my advice is, remove all the TER from pdb (but the last one), leave the
> chain id and use pdb2gmx
> with the option -chainsep ter. The result is supposed to be a topology
> where your chain are grouped in
> a single molecule,making possible to create the bridge, and at the same
> time you keep the chain name
> for future analysis.
>
> Francesco
>
>
> 2013/3/19 shahid nayeem 
>
>> Hi
>> To be more clear I have .xtc file for a disulfide linked complex of
>> two chains. From this trajectory I can extract .xtc file for
>> individual chains. But when I generate .top file from individual chain
>> pdb I get one atom extra in .top file i.e. protonated SG of Cys which
>> I dont need in order to make my .xtc and .top file compatible.
>> Shahid
>>
>> On Tue, Mar 19, 2013 at 2:07 AM, Justin Lemkul  wrote:
>> >
>> >
>> > On 3/18/13 12:35 PM, shahid nayeem wrote:
>> >>
>> >> Hi
>> >> Is it possible to write .top file from .xtc and .tpr using index.ndx
>> >> so that .top is available for tailormade components of simulated
>> >> protein.
>> >>
>> >
>> > All topology information is in the .tpr, but not in .top format.  You
>> may be
>> > able to post-process the output of gmxdump to produce some hacked
>> version,
>> > but that's just a bit of a hand-waving guess.  I don't really understand
>> > what your objective is.
>> >
>> > -Justin
>> >
>> > --
>> > 
>> >
>> > Justin A. Lemkul, Ph.D.
>> > Research Scientist
>> > 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 listgmx-users@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-requ...@gromacs.org.
>> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>> --
>> gmx-users mailing listgmx-users@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-requ...@gromacs.org.
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>
>
>
> --
> Cordiali saluti, Dr.Oteri Francesco
> --
> gmx-users mailing listgmx-users@gromacs.org
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Re: [gmx-users] .top file from .tpr and .xtc

[shahid nayeem]

Hi
To be more clear I have .xtc file for a disulfide linked complex of
two chains. From this trajectory I can extract .xtc file for
individual chains. But when I generate .top file from individual chain
pdb I get one atom extra in .top file i.e. protonated SG of Cys which
I dont need in order to make my .xtc and .top file compatible.
Shahid

On Tue, Mar 19, 2013 at 2:07 AM, Justin Lemkul  wrote:
>
>
> On 3/18/13 12:35 PM, shahid nayeem wrote:
>>
>> Hi
>> Is it possible to write .top file from .xtc and .tpr using index.ndx
>> so that .top is available for tailormade components of simulated
>> protein.
>>
>
> All topology information is in the .tpr, but not in .top format.  You may be
> able to post-process the output of gmxdump to produce some hacked version,
> but that's just a bit of a hand-waving guess.  I don't really understand
> what your objective is.
>
> -Justin
>
> --
> 
>
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> 
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Re: [gmx-users] topology

[shahid nayeem]

I am using Gromacs-4.5.4 and this does not have -cys option in pdb2gmx.
shahid

On Tue, Mar 19, 2013 at 2:06 AM, Justin Lemkul  wrote:
>
>
> On 3/18/13 10:39 AM, shahid nayeem wrote:
>>
>> Hi All
>>   How can I get a topology file using pdb2gmx from a single chain
>> polypeptide with one of the CYS, SH in the form of SG as if it is
>> involved in disulfide linkage, while the other chain with which I
>> expect it to form disulfide link is not in the input pdb file. or can
>> I use pdb2gmx command and get the separate .top and .gro file for each
>> chain using index file.
>>
>
> You may be able to use the -cys option to fool pdb2gmx, but I don't know if
> that will cause problems.  Having half a disulfide present is odd, though
> some force fields support thiolate or neutral (i.e. radical) forms of
> cysteine.  You'll have to look into the force field files to see what's
> available.
>
> -Justin
>
> --
> 
>
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> 
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[gmx-users] topology

[shahid nayeem]

Hi All
 How can I get a topology file using pdb2gmx from a single chain
polypeptide with one of the CYS, SH in the form of SG as if it is
involved in disulfide linkage, while the other chain with which I
expect it to form disulfide link is not in the input pdb file. or can
I use pdb2gmx command and get the separate .top and .gro file for each
chain using index file.

shahid
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Re: [gmx-users] boundwaters

[shahid nayeem]

Hi Justin
 If I use the boundwaters.ndx to write another .ndx file using 1 & 2 &
3 & 4 and so on over all snapshots then also I should get the common
water molecules in these snapshots. Am I right.
Shahid

On Mon, Jan 28, 2013 at 9:03 PM, Justin Lemkul  wrote:
>
>
> On 1/28/13 10:02 AM, shahid nayeem wrote:
>>
>> Dear Users
>> I am interested in knowing only the  water molecules which remains
>> bounded to the protein during MD. Using g_select I can make a
>> boundwater.ndx file which gives water molecules within a specified
>> distance from the protein but it gives different water molecule from
>> each snapshot. Now I want onle those water which is common in all
>> frames. How to proceed from here and is there any other way to do
>> this. Please help.
>
>
> You should be able to write a simple script that runs through each group,
> stores the atom numbers, and then checks which ones are common to all
> frames.
>
> -Justin
>
> --
> 
>
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> 
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[gmx-users] building_insertion_mutants

[shahid nayeem]

Dear all
I am repeating this mail as it could not get uploaded on site. Please
suggest me that whether I can insert 15 residue sequence in an
existing pdb file and can I get the minimized altered coordinates from
here. If not then please suggest an external software or server where
I can model this protein and get the pdb of protein with inserted
peptide segment.
shahid Nayeem
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[gmx-users] Generating insertion mutants

[shahid nayeem]

Dear all
Please suggest me a tool with which I can generate insertion mutants
from a .pdb file. I want to insert new 10-15 aa sequence of AA in
between an existing  .pdb file. The tool should write a new .pdb file
with altered coordinates after insertion of new sequence and
minimization of the structure.
shahid
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Re: [gmx-users] LINCS

[shahid nayeem]

I want to simulate without building the missing residue. Does gromacs
have an option of capping. I am using Gromacs 4.5.4. If not then
suggest some software which I may use.
Shahid nayeem

On Fri, Aug 17, 2012 at 10:03 AM, Mark Abraham  wrote:
> On 17/08/2012 2:28 PM, shahid nayeem wrote:
>>
>> Right, I have a pdb where some of the residues are missing and when I
>> try to simulate it I get LINCS warning in between the atom of the two
>> ends of missing residues. So if I use a smaller time step (0.01) for
>> final production run and energy minimization with setting constraint =
>> none, making it computationally more expensive. Will these results
>> will be O.K.
>
>
> Does it sound OK to model missing residues with solvent (or vacuum) and have
> a chemical bond between the dangling ends? It's also definitely not OK to
> ignore the warning pdb2gmx gave you about this bond being too long. Plowing
> ahead blindly costs more time than than being careful and painstaking.
>
> You need to either cap your chains or build in the missing residues with
> non-GROMACS software, but what's best depends what you're trying to observe.
>
> Mark
>
>
>> Shahid Nayeem
>>
>> On Fri, Aug 17, 2012 at 9:37 AM, Mark Abraham 
>> wrote:
>>>
>>> On 17/08/2012 2:02 PM, shahid nayeem wrote:
>>>>
>>>> Dear all
>>>>>
>>>>> One basic clarification. How does LINCS algorithm influences the
>>>>> results
>>>>> of final production run. In what respect a minimization, pr and final
>>>>> simulation done with constraints = none and with constraint= all_bonds
>>>>> are
>>>>> different.
>>>
>>>
>>> Sounds like you should do some background reading on how and why
>>> constraints
>>> work. Manual and refs therein are good starting points. Or your favourite
>>> molecular simulation textbook. In a nutshell, you use them in production
>>> simulation because they're a reasonable model and allow a larger time
>>> step.
>>> You might avoid them when you're not yet at equilbrium, because their
>>> implementation can be brittle when your structure doesn't agree with the
>>> model physics.
>>>
>>> Mark
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Re: [gmx-users] LINCS

[shahid nayeem]

Right, I have a pdb where some of the residues are missing and when I
try to simulate it I get LINCS warning in between the atom of the two
ends of missing residues. So if I use a smaller time step (0.01) for
final production run and energy minimization with setting constraint =
none, making it computationally more expensive. Will these results
will be O.K.
Shahid Nayeem

On Fri, Aug 17, 2012 at 9:37 AM, Mark Abraham  wrote:
> On 17/08/2012 2:02 PM, shahid nayeem wrote:
>>
>> Dear all
>>>
>>> One basic clarification. How does LINCS algorithm influences the results
>>> of final production run. In what respect a minimization, pr and final
>>> simulation done with constraints = none and with constraint= all_bonds
>>> are
>>> different.
>
>
> Sounds like you should do some background reading on how and why constraints
> work. Manual and refs therein are good starting points. Or your favourite
> molecular simulation textbook. In a nutshell, you use them in production
> simulation because they're a reasonable model and allow a larger time step.
> You might avoid them when you're not yet at equilbrium, because their
> implementation can be brittle when your structure doesn't agree with the
> model physics.
>
> Mark
> --
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[gmx-users] LINCS

[shahid nayeem]

Dear all
> One basic clarification. How does LINCS algorithm influences the results
> of final production run. In what respect a minimization, pr and final
> simulation done with constraints = none and with constraint= all_bonds are
> different.
> Shahid Nayeem
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[gmx-users] Generating_tpr_file from.xtc

[shahid nayeem]

Dear users
By mistake I have deleted my .tpr file after running simulation. Is it
possible to generate .tpr file from .xtc .gro .log and .ene file of final
production run.
shahid Nayeem
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Re: [gmx-users] Umbrella_pull_simulation

[shahid nayeem]

The similar files for wt can be assesed at
 http://www.freefilehosting.net/umbrellawt
 I expected wild type binding energy to be less than mutant
The command used for g_wham is
 g_wham_mpi_4.5.4  -it tpr-files.dat -if pullf-files.dat -o profile_mut.xvg
-hist histo_mut.xvg -unit kCal -b 500 -nBootstrap 200 -bsres
bsResult_mut.xvg -bsprof bsprofile_mut.xvg  -ac
I get the values exactly opposite to my expectation and unable to find out
where I am wrong please suggest.
Shahid Nayeem

On Thu, Mar 15, 2012 at 3:31 PM, shahid nayeem  wrote:

> I have added some new windows in mutant umbrella sampling which removes
> the sampling gap around 4 nm. Also I sampled more windows in the initial
> COM distance in the hope that I get energy minimum of profile well defined.
> I also did boot strapping for error estimates. The files can be assessed at
> http://www.freefilehosting.net/umbrellamut
>
>
> On Wed, Mar 7, 2012 at 4:38 PM, Justin A. Lemkul  wrote:
>
>>
>>
>> shahid nayeem wrote:
>>
>>> The attached profile.xvg and histo.xvg are here.
>>> sorry for sending earlier mail without attachments
>>> Shahid Nayeem
>>>
>>> On Wed, Mar 7, 2012 at 3:25 PM, shahid nayeem >> msnay...@gmail.com>> wrote:
>>>
>>>As suggested by you I added some new window and extended some
>>>simulation and I got the attached profile and histo file. Please see
>>>these files. Experimentally it is known that wt protein-protein
>>>interaction is stronger than the mutants. But I get here is reverse.
>>>what could be the possible reason for it. My profile.xvg and
>>>histo.xvg are right or they need more improvement.
>>>
>>
>> I wouldn't base any conclusions off of them.  You have a sampling gap at
>> just over 4 nm in the mutant simulations.  More importantly, you do not
>> have a defined energy minimum in the mutant windows so it is impossible to
>> calculate a reliable value for DeltaG.  Moreover, in the absence of any
>> error estimates, you can't make any conclusions about these data.  g_wham
>> can generate error bars for you; I'd suggest you do it.
>>
>> -Justin
>>
>> Shahid Nayeem
>>>
>>>
>>>On Tue, Feb 28, 2012 at 7:44 PM, Justin A. Lemkul >><mailto:jalem...@vt.edu>> wrote:
>>>
>>>
>>>
>>>shahid nayeem wrote:
>>>
>>>Thanks. But Does that mean that I should look in pullf.xvg
>>>of each window and see whether the value is converged or
>>>not. If not then I should extend the simulation.
>>>
>>>
>>>I've already made numerous suggestions.  The value in pullf.xvg
>>>is a consequence of the nature of the system.  Looking at the
>>>interactions between your proteins, the stability of those
>>>proteins, etc. is far more informative, like you would for any
>>>simulation (even those that do not make use of the pull code).
>>>
>>>
>>>-Justin
>>>
>>>-- ==**__==
>>>
>>>
>>>Justin A. Lemkul
>>>Ph.D. Candidate
>>>ICTAS Doctoral Scholar
>>>MILES-IGERT Trainee
>>>Department of Biochemistry
>>>Virginia Tech
>>>Blacksburg, VA
>>>jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
>>>
>>> http://www.bevanlab.biochem.__**vt.edu/Pages/Personal/justin<http://vt.edu/Pages/Personal/justin>
>>>
>>> <http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>>> >
>>>
>>>==**__==
>>>-- gmx-users mailing listgmx-users@gromacs.org
>>><mailto:gmx-users@gromacs.org>
>>>
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Re: [gmx-users] Umbrella_pull_simulation

[shahid nayeem]

I have added some new windows in mutant umbrella sampling which removes the
sampling gap around 4 nm. Also I sampled more windows in the initial COM
distance in the hope that I get energy minimum of profile well defined. I
also did boot strapping for error estimates. The files can be assessed at
http://www.freefilehosting.net/umbrellamut


On Wed, Mar 7, 2012 at 4:38 PM, Justin A. Lemkul  wrote:

>
>
> shahid nayeem wrote:
>
>> The attached profile.xvg and histo.xvg are here.
>> sorry for sending earlier mail without attachments
>> Shahid Nayeem
>>
>> On Wed, Mar 7, 2012 at 3:25 PM, shahid nayeem > msnay...@gmail.com>> wrote:
>>
>>As suggested by you I added some new window and extended some
>>simulation and I got the attached profile and histo file. Please see
>>these files. Experimentally it is known that wt protein-protein
>>interaction is stronger than the mutants. But I get here is reverse.
>>what could be the possible reason for it. My profile.xvg and
>>histo.xvg are right or they need more improvement.
>>
>
> I wouldn't base any conclusions off of them.  You have a sampling gap at
> just over 4 nm in the mutant simulations.  More importantly, you do not
> have a defined energy minimum in the mutant windows so it is impossible to
> calculate a reliable value for DeltaG.  Moreover, in the absence of any
> error estimates, you can't make any conclusions about these data.  g_wham
> can generate error bars for you; I'd suggest you do it.
>
> -Justin
>
> Shahid Nayeem
>>
>>
>>On Tue, Feb 28, 2012 at 7:44 PM, Justin A. Lemkul ><mailto:jalem...@vt.edu>> wrote:
>>
>>
>>
>>shahid nayeem wrote:
>>
>>Thanks. But Does that mean that I should look in pullf.xvg
>>of each window and see whether the value is converged or
>>not. If not then I should extend the simulation.
>>
>>
>>I've already made numerous suggestions.  The value in pullf.xvg
>>is a consequence of the nature of the system.  Looking at the
>>interactions between your proteins, the stability of those
>>proteins, etc. is far more informative, like you would for any
>>simulation (even those that do not make use of the pull code).
>>
>>
>>-Justin
>>
>>-- ==**__==
>>
>>
>>Justin A. Lemkul
>>Ph.D. Candidate
>>ICTAS Doctoral Scholar
>>MILES-IGERT Trainee
>>Department of Biochemistry
>>Virginia Tech
>>Blacksburg, VA
>>jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
>>
>> http://www.bevanlab.biochem.__**vt.edu/Pages/Personal/justin<http://vt.edu/Pages/Personal/justin>
>>
>> <http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>> >
>>
>>==**__==
>>-- gmx-users mailing listgmx-users@gromacs.org
>><mailto:gmx-users@gromacs.org>
>>
>> http://lists.gromacs.org/__**mailman/listinfo/gmx-users<http://lists.gromacs.org/__mailman/listinfo/gmx-users>
>>
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>> >
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>>
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>> before
>>posting!
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>>
>>
>>
> --
> ==**==
>
> 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
&g

Re: [gmx-users] Umbrella_pull_simulation

[shahid nayeem]

As suggested by you I added some new window and extended some simulation
and I got the attached profile and histo file. Please see these files.
Experimentally it is known that wt protein-protein interaction is stronger
than the mutants. But I get here is reverse. what could be the possible
reason for it. My profile.xvg and histo.xvg are right or they need more
improvement.
Shahid Nayeem

On Tue, Feb 28, 2012 at 7:44 PM, Justin A. Lemkul  wrote:

>
>
> shahid nayeem wrote:
>
>> Thanks. But Does that mean that I should look in pullf.xvg of each window
>> and see whether the value is converged or not. If not then I should extend
>> the simulation.
>>
>
> I've already made numerous suggestions.  The value in pullf.xvg is a
> consequence of the nature of the system.  Looking at the interactions
> between your proteins, the stability of those proteins, etc. is far more
> informative, like you would for any simulation (even those that do not make
> use of the pull code).
>
>
> -Justin
>
> --
> ==**==
>
> 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
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>
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Re: [gmx-users] Umbrella_pull_simulation

[shahid nayeem]

Thanks. But Does that mean that I should look in pullf.xvg of each window
and see whether the value is converged or not. If not then I should extend
the simulation.
Shahid Nayeem

On Sat, Feb 25, 2012 at 12:05 AM, Justin A. Lemkul  wrote:

>
>
> shahid nayeem wrote:
>
>> My protein complex interface has a hydrophobic core and on each side of
>> this core at the edge are two hydrogen bonds. The Hydrogen bond on one side
>> is between Arg and Asp and another side it is between Arg and Glu. Its
>> experimental Kd is in nanomolar regions. How should I decide the length of
>> the simulation required in each window with this information.
>>
>
> As you would any other system.  Look for convergence of observables of
> interest.  Your PMF alone suggests insufficient sampling for these
> simulations, so as I've said several times, you probably need longer
> simulations to do so, but you can start by examining the physical
> properties of each window.  What you're looking for is up to you, based on
> your knowledge of the system at hand.
>
>
> -Justin
>
> --
> ==**==
>
> 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<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>
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Re: [gmx-users] Umbrella_pull_simulation

[shahid nayeem]

My protein complex interface has a hydrophobic core and on each side of
this core at the edge are two hydrogen bonds. The Hydrogen bond on one side
is between Arg and Asp and another side it is between Arg and Glu. Its
experimental Kd is in nanomolar regions. How should I decide the length of
the simulation required in each window with this information.
Shahid nayeem

On Fri, Feb 24, 2012 at 7:56 PM, Justin A. Lemkul  wrote:

>
>
> shahid nayeem wrote:
>
>> I thought this time to be sufficient without any reasonable basis.
>>
>
> If you pick an arbitrary time frame, you're going to get results with
> arbitrary accuracy.  Your time frame should be decided based on a whole
> host of factors, not the least of which include an assessment of the types
> of interactions in the system and how they may decay as a function of
> distance, as well as the individual convergence of observables in each
> simulation.  This is true of any simulation.  Only after you can conclude
> that each window has converged can you expect to draw any reasonable
> conclusions.
>
>
> -Justin
>
> --
> ==**==
>
> 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<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>
> ==**==
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Re: [gmx-users] Umbrella_pull_simulation

[shahid nayeem]

I thought this time to be sufficient without any reasonable basis.
shahid Nayeem

On Fri, Feb 24, 2012 at 7:40 PM, Justin A. Lemkul  wrote:

>
>
> shahid nayeem wrote:
>
>> My system is a  protein-protein complex. After pulling I selected windows
>> at 0.1nm from an initial COM distance of 3.65nm to 5.7nm and thereafter
>> windows at 0.2nm spacing was selected  upto 7.5nm. In each window 10ns MD
>> was done and g_wham command was run neglecting the fist 1ns run for
>> equilibriation.
>>
>
> OK, so how did you decide that 10 ns was sufficient in each window?
>
> -Justin
>
>
> --
> ==**==
>
> 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<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>
> ==**==
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Re: [gmx-users] Umbrella_pull_simulation

[shahid nayeem]

My system is a  protein-protein complex. After pulling I selected windows
at 0.1nm from an initial COM distance of 3.65nm to 5.7nm and thereafter
windows at 0.2nm spacing was selected  upto 7.5nm. In each window 10ns MD
was done and g_wham command was run neglecting the fist 1ns run for
equilibriation.
Shahid Nayeem

On Tue, Feb 21, 2012 at 6:42 PM, Justin A. Lemkul  wrote:

>
>
> shahid nayeem wrote:
>
>> Initially I used g_wham -if pullf-files.dat -it tpr-files.dat -unit Kcal
>> -histo. But now  as suggested by you I added -b 1000 -e 1 leaving 1ns
>> for equilibriation. The new profile.xvg is attached. How can I further
>> improve it.
>>
>>
> I don't know.  You've never even stated what your system is, how you
> decided on the window spacing or time in each window, etc.  It may be that
> your simulations are too short.  You have a few regions along the reaction
> coordinate that are not well-sampled, which could contribute to some
> rockiness in the PMF.
>
> -Justin
>
>  Shahid Nayeem
>>
>>
>> On Tue, Feb 21, 2012 at 1:04 AM, Justin A. Lemkul > jalem...@vt.edu>> wrote:
>>
>>
>>
>>shahid nayeem wrote:
>>
>>I am attaching a profile.xvg and histo.xvg. In each window 10ns
>>sampling was done. The umbrella pullcode used is as follows.
>>; Pull code
>>pull= umbrella
>>pull_geometry   = distance  ; simple distance increase pull_dim
>>   = YN Y
>>pull_vec1   = 0.75 0 1
>>pull_start  = yes   ; define initial COM distance > 0
>>pull_ngroups= 1
>>pull_group0 = Chain_B pull_group1 = Chain_A pull_rate1
>> = 0.01  ; 0.01 nm per ps = 10 nm per ns
>>pull_k1 = 1000  ; kJ mol^-1 nm^-2
>>
>>Please tell me my profile.xvg and histo.xvg are fine or not. In
>>profile.xvg why i am not getting smooth convergence.
>>
>>
>>They're not terrible, but could be better.  The PMF profile is a
>>little rough and there are some regions of the reaction coordinate
>>with little sampling. Maybe your simulations need to be longer
>>and/or you need to exclude some amount of time at the beginning of
>>each as equilibration (which you probably should do anyway, but
>>without seeing your g_wham command, there's no way to know what you
>>may or may not be considering).
>>
>>-Justin
>>
>>Shahid Nayeem
>>
>>
>>On Mon, Feb 20, 2012 at 8:24 PM, Justin A. Lemkul
>>mailto:jalem...@vt.edu>
>><mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>>> wrote:
>>
>>
>>
>>   shahid nayeem wrote:
>>
>>   Thanks Justin
>>   I have pulled one of the chain from an initial COM distance
>>   value of 3.65 A to 7.90 A. When I look this trajectory in
>>VMD I
>>   find that the
>>
>>
>>   I will have to assume you mean nm.  Gromacs does not deal in
>>   Angstrom, and these distances would be within any sensible
>>   short-range cutoff and thus not indicative of actual separation.
>>
>>
>>   chain is completely separated. But even at this
>>separation the
>>   profile.xvg file does not show its convergence to one
>>value. I
>>   sent this file to you earlier.
>>
>>
>>   Sorry, I don't have a photographic memory, nor can I recall if
>>   you've ever posted your .mdp file, or at the very least, told
>>us how
>>   much sampling you've done in each window.  It may well be
>>that your
>>   simulations are simply too short to observe adequate
>>   post-equilibration sampling.
>>
>>
>>   -Justin
>>
>>   -- ==**==
>>
>>
>>
>>   Justin A. Lemkul
>>   Ph.D. Candidate
>>   ICTAS Doctoral Scholar
>>   MILES-IGERT Trainee
>>   Department of Biochemistry
>>   Virginia Tech
>>   Blacksburg, VA
>>   jalemkul[at]vt.edu <http://vt.edu> <http://vt.edu> | (540)
>>231-9080
>>   http://www.bevanlab.biochem.__**__vt.edu/Pages/Personal/justin
>>
>> <http://vt.edu/Pages/Personal/**justin<http://vt.edu/Pages/Personal/justin&g

Re: [gmx-users] Umbrella_pull_simulation

[shahid nayeem]

Initially I used g_wham -if pullf-files.dat -it tpr-files.dat -unit Kcal
-histo. But now  as suggested by you I added -b 1000 -e 1 leaving 1ns
for equilibriation. The new profile.xvg is attached. How can I further
improve it.

Shahid Nayeem

On Tue, Feb 21, 2012 at 1:04 AM, Justin A. Lemkul  wrote:

>
>
> shahid nayeem wrote:
>
>> I am attaching a profile.xvg and histo.xvg. In each window 10ns sampling
>> was done. The umbrella pullcode used is as follows.
>> ; Pull code
>> pull= umbrella
>> pull_geometry   = distance  ; simple distance increase pull_dim=
>> YN Y
>> pull_vec1   = 0.75 0 1
>> pull_start  = yes   ; define initial COM distance > 0
>> pull_ngroups= 1
>> pull_group0 = Chain_B pull_group1 = Chain_A pull_rate1  =
>> 0.01  ; 0.01 nm per ps = 10 nm per ns
>> pull_k1 = 1000  ; kJ mol^-1 nm^-2
>>
>> Please tell me my profile.xvg and histo.xvg are fine or not. In
>> profile.xvg why i am not getting smooth convergence.
>>
>
> They're not terrible, but could be better.  The PMF profile is a little
> rough and there are some regions of the reaction coordinate with little
> sampling. Maybe your simulations need to be longer and/or you need to
> exclude some amount of time at the beginning of each as equilibration
> (which you probably should do anyway, but without seeing your g_wham
> command, there's no way to know what you may or may not be considering).
>
> -Justin
>
>  Shahid Nayeem
>>
>>
>> On Mon, Feb 20, 2012 at 8:24 PM, Justin A. Lemkul > jalem...@vt.edu>> wrote:
>>
>>
>>
>>shahid nayeem wrote:
>>
>>Thanks Justin
>>I have pulled one of the chain from an initial COM distance
>>value of 3.65 A to 7.90 A. When I look this trajectory in VMD I
>>find that the
>>
>>
>>I will have to assume you mean nm.  Gromacs does not deal in
>>Angstrom, and these distances would be within any sensible
>>short-range cutoff and thus not indicative of actual separation.
>>
>>
>>chain is completely separated. But even at this separation the
>>profile.xvg file does not show its convergence to one value. I
>>sent this file to you earlier.
>>
>>
>>Sorry, I don't have a photographic memory, nor can I recall if
>>you've ever posted your .mdp file, or at the very least, told us how
>>much sampling you've done in each window.  It may well be that your
>>simulations are simply too short to observe adequate
>>post-equilibration sampling.
>>
>>
>>-Justin
>>
>>-- ==**__==
>>
>>
>>Justin A. Lemkul
>>Ph.D. Candidate
>>ICTAS Doctoral Scholar
>>MILES-IGERT Trainee
>>Department of Biochemistry
>>Virginia Tech
>>Blacksburg, VA
>>jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
>>
>> http://www.bevanlab.biochem.__**vt.edu/Pages/Personal/justin<http://vt.edu/Pages/Personal/justin>
>>
>> <http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>> >
>>
>>==**__==
>>
>>-- gmx-users mailing listgmx-users@gromacs.org
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>> >
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>>
>>
> --
> ===

Re: [gmx-users] Umbrella_pull_simulation

[shahid nayeem]

I am attaching a profile.xvg and histo.xvg. In each window 10ns sampling
was done. The umbrella pullcode used is as follows.
; Pull code
pull= umbrella
pull_geometry   = distance  ; simple distance increase
pull_dim= YN Y
pull_vec1   = 0.75 0 1
pull_start  = yes   ; define initial COM distance > 0
pull_ngroups= 1
pull_group0 = Chain_B
pull_group1 = Chain_A
pull_rate1  = 0.01  ; 0.01 nm per ps = 10 nm per ns
pull_k1 = 1000  ; kJ mol^-1 nm^-2

Please tell me my profile.xvg and histo.xvg are fine or not. In profile.xvg
why i am not getting smooth convergence.
Shahid Nayeem

On Mon, Feb 20, 2012 at 10:48 PM, shahid nayeem  wrote:

> I am attaching a profile.xvg and histo.xvg. In each window 10ns sampling
> was done. The umbrella pullcode used is as follows.
> ; Pull code
> pull= umbrella
> pull_geometry   = distance  ; simple distance increase
> pull_dim= YN Y
> pull_vec1   = 0.75 0 1
> pull_start  = yes   ; define initial COM distance > 0
> pull_ngroups= 1
> pull_group0 = Chain_B
> pull_group1 = Chain_A
> pull_rate1  = 0.01  ; 0.01 nm per ps = 10 nm per ns
> pull_k1 = 1000  ; kJ mol^-1 nm^-2
>
> Please tell me my profile.xvg and histo.xvg are fine or not. In
> profile.xvg why i am not getting smooth convergence.
> Shahid Nayeem
>
> On Mon, Feb 20, 2012 at 8:24 PM, Justin A. Lemkul  wrote:
>
>>
>>
>> shahid nayeem wrote:
>>
>>> Thanks Justin
>>> I have pulled one of the chain from an initial COM distance value of
>>> 3.65 A to 7.90 A. When I look this trajectory in VMD I find that the
>>>
>>
>> I will have to assume you mean nm.  Gromacs does not deal in Angstrom,
>> and these distances would be within any sensible short-range cutoff and
>> thus not indicative of actual separation.
>>
>>
>>  chain is completely separated. But even at this separation the
>>> profile.xvg file does not show its convergence to one value. I sent this
>>> file to you earlier.
>>>
>>
>> Sorry, I don't have a photographic memory, nor can I recall if you've
>> ever posted your .mdp file, or at the very least, told us how much sampling
>> you've done in each window.  It may well be that your simulations are
>> simply too short to observe adequate post-equilibration sampling.
>>
>>
>> -Justin
>>
>> --
>> ==**==
>>
>> 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<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>>
>> ==**==
>> --
>> gmx-users mailing listgmx-users@gromacs.org
>> http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users>
>> Please search the archive at http://www.gromacs.org/**
>> Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>before
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>>
>
>


profile.xvg
Description: Binary data
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Re: [gmx-users] Umbrella_pull_simulation

[shahid nayeem]

Thanks Justin
I have pulled one of the chain from an initial COM distance value of 3.65 A
to 7.90 A. When I look this trajectory in VMD I find that the chain is
completely separated. But even at this separation the profile.xvg file does
not show its convergence to one value. I sent this file to you earlier.
shahid Nayeem

On Sat, Feb 18, 2012 at 7:27 PM, Justin A. Lemkul  wrote:

>
>
> shahid nayeem wrote:
>
>> Dear All
>>
>> I am doing umbrella sampling for a protein complex. After analysis I am
>> finding that prifle.xvg has not converged. Now I want to extend simulation.
>> I have already pulled one chain to the length of the box. Can I further
>> pull by extending the box size and add more windows to umbrella sampling.
>> Please suggest.
>>
>
> You would have to use a simple test system to prove that this is a valid
> approach.  Changing the nature of the system for some windows sounds very
> questionable to me, and likely would be to reviewers.
>
>
>  How one should ascertain the initial box size so that g_wham gives a
>> converged profile.xvg.
>>
>
> You should determine the distance needed to sufficiently separate your
> components, that is, determine the minimum COM distance at which
> interaction between the two species is negligible.  Ideally, they would be
> non-interacting, but with PME, that is not possible.
>
> -Justin
>
> --
> ==**==
>
> 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<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>
> ==**==
> --
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[gmx-users] Umbrella_pull_simulation

[shahid nayeem]

Dear All

I am doing umbrella sampling for a protein complex. After analysis I am
finding that prifle.xvg has not converged. Now I want to extend simulation.
I have already pulled one chain to the length of the box. Can I further
pull by extending the box size and add more windows to umbrella sampling.
Please suggest.
How one should ascertain the initial box size so that g_wham gives a
converged profile.xvg.
Please help.
Shahid nayeem
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[gmx-users] Umbrella_pulling_simulation

[shahid nayeem]

Dear All
 How does the terminal group capping/ionization state will influence the
Free energy obtained from g_wham in umbrella sampling simulation.
Shahid Nayeem
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Re: [gmx-users] Number of windows in umbrella sampling

[shahid nayeem]

Thanks Justin. I will try again. But please refer to some protocol if you
know and one last question that before doing umbrella sampling simulation
how can one be sure that the pulling is good and one should go ahead with
selecting window and doing umbrella sampling. In the end when you see
histo.xvg and profile.xvg , it cost a lot computationally and if you
 don't get it right these computational resources are wasted.
Shahid nayeem

On Mon, Feb 13, 2012 at 8:12 PM, Justin A. Lemkul  wrote:

>
>
> shahid nayeem wrote:
>
>> Thanks for quick reply. I have created mutant of a complex by changing
>> interface residue in VMD. These mutant are experimentally known to show
>> less binding affinity. I want to reproduce these results with umbrella
>> sampling. Now I am sending profile and histo file for wt and mutant. Please
>> suggest where i am wrong.
>>
>
> The PMF curves look poorly converged.  Your reaction coordinates are not
> the same for both the WT and mutant (you appear to have a far shorter
> reaction coordinate for the mutant).  The energy minimum is also
> ill-defined for the mutant.
>
> As for the reason behind these phenomena, I cannot say, nor do I have time
> to sort through your data and try to work it out for you.  Refer to the
> literature, find similar protocols, and proceed from there.
>
> -Justin
>
>  Shahid Nayeem
>>
>>
>> On Mon, Feb 13, 2012 at 7:15 PM, Justin A. Lemkul > jalem...@vt.edu>> wrote:
>>
>>
>>
>>shahid nayeem wrote:
>>
>>Dear Justin
>>I am doing umbrella pulling simulation of a protein complex wt
>>and mutant. I expect mutant to give lower deltG value. I am
>>attaching a tif file of energy vs time curve of wt and mutant
>>protein on pulling simulation. These energies are obtained by
>>g_energy and selecting 11 option which is COM pulling energy. In
>>this curve the first peak decreases and again rises at longer
>>time. How many windows should be selected. As expected the peak
>>of COM pulling energy is lower in mutants. Please explain why
>>the energy again rises at higher time. Should I use the windows
>>upto 160ps only because thereafter in both curve there is rise
>>in energy value. the pull code used is as follows.
>>
>>
>>What you have obtained is a path-dependent energy that may or may
>>not signify anything useful - it almost certainly does not.  I
>>cannot offer an explanation of the sharp increase towards the end of
>>the simulation other than to speculate that your box is of
>>insufficient size and you're encountering PBC issues.
>>
>>As for how many windows are necessary, it's also impossible to tell.
>> You need enough windows to adequately sample the reaction
>>coordinate.  Thus, it is decided based on how far you need to
>>separate the two species, how strong the force constant is during
>>the US simulations, the nature of the interactions in the system and
>>how fast they converge, etc.
>>
>>-Justin
>>
>>
>>pull_geometry   = distance pull_dim= Y N  Y
>>pull_vec1   = 0.75 0  1
>>pull_start  = yes  pull_ngroups= 1
>>pull_group0 = Chain_B pull_group1 = Chain_A pull_rate1
>> = 0.01  pull_k1 = 1000
>>
>>-- ==**__==
>>
>>
>>Justin A. Lemkul
>>Ph.D. Candidate
>>ICTAS Doctoral Scholar
>>MILES-IGERT Trainee
>>Department of Biochemistry
>>Virginia Tech
>>Blacksburg, VA
>>jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
>>
>> http://www.bevanlab.biochem.__**vt.edu/Pages/Personal/justin<http://vt.edu/Pages/Personal/justin>
>>
>> <http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>> >
>>
>>==**__==
>>
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>><mailto:gmx-users@gromacs.org>
>>
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>> >
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>>
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Re: [gmx-users] Using shell script to analyze the results

[shahid nayeem]

Create a file named input.g_rms. write the group number in this file. In
your shell script after command line write  wrote:

> Hi,
>
> I'm not good at shell programming now.
> For the simplicity, I wrote down all the gromacs commands in one shell
> script.
>
> It means that if I execute the .sh file, then every works including graphs
> used for analysis are done.
> However, when there are g_msd -f *.xtc -s *.tpr -o *.xvg -rmcomm, I have
> to select the groups manually.
> This is quite inconvenient...
>
> Is there any way to handle this??
>
> Thanks in advance
>
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[gmx-users] Running_crashed_run

[shahid nayeem]

Dear all
I am using Gromacs-4.5.4 . when I restart a crashed run after generating a
new .tpr with tpbconv ,it does not run without giving the option of
-noappend. How to run this with -append option. as far as I know in all
version of 4.x onward -append is default option but it does not works in my
case. Thanks for any help.
Shahid Nayeem
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[gmx-users] tip3p water in gromacs_4.5.4

[shahid nayeem]

Dear all
I want to use tip3p water model for solvating my protein with genbox
command . I couldnt find tip3p.gro file in Gromacs/share/top folder .
please help me
I am following using command
genbox -cp protein_box.gro -cs tip3p.gro -o solv.gro -p *.top
It says tip3p.gro not found.
Please help.
shahid Nayeem
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[gmx-users] topology and parameter for cobalt metal

[shahid nayeem]

Dear all
I am interested in simulating a model protein with cobalt forming
coordinate bond with His. I coud'nt find entry for cobalt in any forcefield
.rtp file. I am using Gromacs 4.5.4 . If any one can help me in getting
forcefield parameters for charmm27/ OPLSaa/Amber99 in gromacs format please
respond. Please suggest where else I should search for these.
Thanking all
shahid Nayeem
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Re: [gmx-users] RMSD

[shahid nayeem]

Thanks. But in timeline plugin of VMD I am able to measure RMSD with
respect to one of the frame of trajectory and I am interested to measure
RMSD with respect to another molecule. I am trying to measure RMSD of
trajectory frames with respect to Bound and unbound configuration of
molecule so that I can compare side chain configuration of trajectory with
bound and unbound sidechain configuration.  Please help.
Shahid Nayeem

On Tue, Nov 15, 2011 at 7:02 PM, felmer...@uchile.cl wrote:

> In any case, if you really want to see flexibility then you need RMSF and
> not RMSD as the later will only tell you about how similar is the
> configuration of a sidechain compared to a reference frame. If that is
> still what you want i think VMD has a tool for that in the timeline plugin.
>
>
>
> regards
>
>
>
> Felipe
>
> Mensaje original
> De: gianluca.sant...@ibs.fr
> Fecha: 15-nov-2011 10:18
> Para: "Discussion list for GROMACS users"
> Asunto: Re: [gmx-users] RMSD
>
>
> On 11/15/11 8:23 PM, shahid nayeem wrote:
>
> Dear all
> I am interested to get contour plot of residue RMSD vs time graph. I want
> to get the flexible and rigid regions of protein chain during simulation.
> g_rmsf does not gives me this plot.
> Please help
> shahid Nayeem
>
>
>
> Try g_rmsf -res , it could be useful, maybe.
>
> --
> Gianluca Santoni,
> Institut de Biologie Structurale
> 41 rue Horowitz
> Grenoble
> _
> Please avoid sending me Word or PowerPoint attachments.
> See http://www.gnu.org/philosophy/no-word-attachments.html
>
>
>
>
> --
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[gmx-users] RMSD

[shahid nayeem]

Dear all
I am interested to get contour plot of residue RMSD vs time graph. I want
to get the flexible and rigid regions of protein chain during simulation.
g_rmsf does not gives me this plot.
Please help
shahid Nayeem
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[gmx-users] Protein_model_refinement

[shahid nayeem]

Dear All
I want to refine a protein homology model, I did minimization but then
procheck does not give better Ramachandran plot. This model is a homodimer
with each chain of 609 residue and a total of 1218 residue so a long MD
simulation to search native state is not feasible. Can any one help me on
this list to tell that how should I attempt this problem.
Shahid Nayeem
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[gmx-users] protein_model_refinement

[shahid nayeem]

Dear All
I am trying to refine a protein model which is a homodimer with each chain
having 609 residues.I tried minimizing in Chimera and then checking models
with procheck.Infact model quality deteriorated as far as Ramachandran plot
is concerned. Will doing MD simulation help me in Gromacs. It is a big
protein so long MD simulation is not possible. Short duration MD will be
insufficient to search native structure. I am stuck-up. Can anyone on this
list help me.
Shahid Nayeem
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Re: [gmx-users] Arginine_Hydrochloride topology

[shahid nayeem]

I tried with single Arginine molecule pdb.
pdb2gmx -f arg.pdb -o arg.gro -p arg.top
genconf -f arg.gro -nbox 2 2 2 -o seq.gro
genbox -cp seq.gro -cs spc216.gro -ci protein.pdb -nmol 1 -o seq_box.gro
-box 1.8 1.8 1.8
command runs but it does not add protein.pdb to the box
shahid nayeem

On Fri, Aug 12, 2011 at 4:32 PM, Justin A. Lemkul  wrote:

>
>
> shahid nayeem wrote:
>
>> I couldn't get you. Does it means that  for pre-positioning say 40
>> molecules of Arginine do I need to create 40 pdb of different coordinate
>> then combine it with pdb of protein and then use pdb2gmx. I want to use
>> different number of free positively charged Arginine molecule in simulation
>> box along with protein.
>> shahid nayeem
>>
>>
> Treat the system like you would any other "normal" protein.  Run pdb2gmx on
> a coordinate file of a single molecule and proceed with building your
> system, which can include replication (i.e. genconf to get multiple
> molecules), genbox (to add other molecules and solvent), and genion.  For
> systems with different numbers of arginine, simply alter the corresponding
> line in the [molecules] directive of the topology that pdb2gmx wrote.
>
> -Justin
>
>  On Thu, Aug 11, 2011 at 3:15 PM, Mark Abraham 
> > mark.abra...@anu.edu.**au >> wrote:
>>
>>On 11/08/2011 7:24 PM, shahid nayeem wrote:
>>
>>>Hi Justin
>>>I prepared a box of SOL and arginine Hydrochloride. But when I
>>>solvate my protein with this box now the positively charged
>>>arginine is as solvent and this causes problem in grompp. It gives
>>>error like "No such Molecule types ARG" etc. Solvating arginine
>>>with water and preparing a box was without error. which forcefield
>>>in gromacs has inbuilt .itp file for free amino acid which I can
>>>include in my .top file.
>>>
>>
>>See 
>> http://www.gromacs.org/**Documentation/How-tos/**Multiple_Chains<http://www.gromacs.org/Documentation/How-tos/Multiple_Chains>
>> .
>>Pre-position the non-water molecules, use pdb2gmx, solvate.
>>
>>Mark
>>
>>
>> Shahid Nayeem
>>>
>>>On Fri, Jul 29, 2011 at 5:02 PM, Justin A. Lemkul >><mailto:jalem...@vt.edu>> wrote:
>>>
>>>
>>>
>>>shahid nayeem wrote:
>>>
>>>Dear All I am trying to find the topology and parameterof
>>>free Arginine Hydrchloride molecule in gromacs force-field
>>>format. Developing it in Pro-Drg will not serve as  I will
>>>need some other parametrization tool to check it charges.
>>>If someone can help, I will be grateful.
>>>
>>>
>>>Isn't this just a protonated arginine (normal state for
>>>neutral pH) with a chloride counterion?  There's nothing
>>>special about it, just run a coordinate file through pdb2gmx
>>>with the force field of your choice.
>>>
>>>-Justin
>>>
>>>-- ==**==
>>>
>>>Justin A. Lemkul
>>>Ph.D. Candidate
>>>ICTAS Doctoral Scholar
>>>MILES-IGERT Trainee
>>>Department of Biochemistry
>>>Virginia Tech
>>>Blacksburg, VA
>>>jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
>>>
>>>
>>> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>>>
>>>==**==
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>>><mailto:gmx-users@gromacs.org>
>>>
>>>
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>>>Please search the archive at
>>>
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>>>posting!
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>>> >.
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Re: [gmx-users] Arginine_Hydrochloride topology

[shahid nayeem]

I couldn't get you. Does it means that  for pre-positioning say 40 molecules
of Arginine do I need to create 40 pdb of different coordinate then combine
it with pdb of protein and then use pdb2gmx. I want to use different number
of free positively charged Arginine molecule in simulation box along with
protein.
shahid nayeem

On Thu, Aug 11, 2011 at 3:15 PM, Mark Abraham wrote:

>  On 11/08/2011 7:24 PM, shahid nayeem wrote:
>
> Hi Justin
> I prepared a box of SOL and arginine Hydrochloride. But when I solvate my
> protein with this box now the positively charged arginine is as solvent and
> this causes problem in grompp. It gives error like "No such Molecule types
> ARG" etc. Solvating arginine with water and preparing a box was without
> error. which forcefield in gromacs has inbuilt .itp file for free amino acid
> which I can include in my .top file.
>
>
> See http://www.gromacs.org/Documentation/How-tos/Multiple_Chains.
> Pre-position the non-water molecules, use pdb2gmx, solvate.
>
> Mark
>
>
>  Shahid Nayeem
>
> On Fri, Jul 29, 2011 at 5:02 PM, Justin A. Lemkul  wrote:
>
>>
>>
>> shahid nayeem wrote:
>>
>>> Dear All I am trying to find the topology and parameterof free Arginine
>>> Hydrchloride molecule in gromacs force-field format. Developing it in
>>> Pro-Drg will not serve as  I will need some other parametrization tool to
>>> check it charges. If someone can help, I will be grateful.
>>>
>>
>>  Isn't this just a protonated arginine (normal state for neutral pH) with
>> a chloride counterion?  There's nothing special about it, just run a
>> coordinate file through pdb2gmx with the force field of your choice.
>>
>> -Justin
>>
>> --
>> 
>>
>> 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
>>
>> 
>>  --
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>>
>
>
>
>
>
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Re: [gmx-users] pmf_calculation

[shahid nayeem]

Both files hist.xvg and profile.xvg both are simultaneous output of this
command. I did not run it twice, once to get profile.xvg and then to get
hist.xvg as you uderstood.

On Thu, Aug 11, 2011 at 5:42 PM, Justin A. Lemkul  wrote:

>
>
> shahid nayeem wrote:
>
>> I used following command
>> g_wham_4.5.4  -it tpr-files.dat -if pullf-files.dat -o hist -unit kCal
>> Both profile.xvg and hist.xvg are created with this command using same
>> pullf.xvg and .tpr files.
>>
>
> An identical command with identical input files producing totally different
> output?  Sorry, but I find that hard to believe.  Check your work and make
> sure you're using the input you think you are.  I suspect something's amiss
> and you're not seeing it.
>
> -Justin
>
>  shahid Nayeem
>>
>>
>> On Thu, Aug 11, 2011 at 5:07 PM, Justin A. Lemkul > jalem...@vt.edu>> wrote:
>>
>>
>>
>>shahid nayeem wrote:
>>
>>Dear Justin
>>
>>I did some more sampling and sending you profile.xvg, histo.xvg.
>>and hist.xvg. I am sending histo.xvg hist.xvg and profile.xvg.
>>please tell my the difference in profile.xvg and hist.xvg. Both
>>should be same but I get different curves here.
>>
>>
>>I can't tell you the difference because you haven't shown how they
>>were generated.  My blind guess is that hist.xvg (a very confusing
>>name for a PMF profile) was generated from data that have poor
>>sampling in two regions.  The contents of profile.xvg look normal.
>> I don't know which of these curves corresponds to histo.xvg,
>>because the histograms therein look fine.
>>
>>Please make sure to give full descriptions of these files.  You've
>>quote a message that is over a month old.  I've replied to hundreds
>>of messages since then and I do not remember the full context of our
>>discussion.
>>
>>-Justin
>>
>>On Tue, Jul 5, 2011 at 5:16 PM, Justin A. Lemkul
>>mailto:jalem...@vt.edu>
>><mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>>> wrote:
>>
>>
>>
>>   shahid nayeem wrote:
>>
>>   Dear Justin
>>   I did pmf calculation for my protein-protein complex
>>using your
>>   tutorial.Off course changing the pull_direction suitable
>>for my
>>   protein but more or less following the same strategy. I
>>am using
>>   gromacs_4.5.4 and g_wham utility. The profile.xvg file
>>which I
>>   get is attached and it shows two dips in PE curve. Please
>>see it
>>   and tell me why I am getting these dips.
>>
>>
>>   You have insufficient sampling in at least these two regions.
>> Your
>>   histograms should confirm this.
>>
>>   -Justin
>>
>>   -- ==**==
>>
>>   Justin A. Lemkul
>>   Ph.D. Candidate
>>   ICTAS Doctoral Scholar
>>   MILES-IGERT Trainee
>>   Department of Biochemistry
>>   Virginia Tech
>>   Blacksburg, VA
>>   jalemkul[at]vt.edu <http://vt.edu> <http://vt.edu> | (540)
>>
>>231-9080
>>
>>   http://www.bevanlab.biochem.__**__vt.edu/Pages/Personal/justin
>>
>> <http://vt.edu/Pages/Personal/**justin<http://vt.edu/Pages/Personal/justin>
>> >
>>
>>   <http://www.bevanlab.biochem._**_vt.edu/Pages/Personal/justin
>>
>> <http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>> >>
>>
>>   ==**==
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Re: [gmx-users] pmf_calculation

[shahid nayeem]

I used following command
g_wham_4.5.4  -it tpr-files.dat -if pullf-files.dat -o hist -unit kCal
Both profile.xvg and hist.xvg are created with this command using same
pullf.xvg and .tpr files.
shahid Nayeem

On Thu, Aug 11, 2011 at 5:07 PM, Justin A. Lemkul  wrote:

>
>
> shahid nayeem wrote:
>
>> Dear Justin
>>
>> I did some more sampling and sending you profile.xvg, histo.xvg. and
>> hist.xvg. I am sending histo.xvg hist.xvg and profile.xvg. please tell my
>> the difference in profile.xvg and hist.xvg. Both should be same but I get
>> different curves here.
>>
>>
> I can't tell you the difference because you haven't shown how they were
> generated.  My blind guess is that hist.xvg (a very confusing name for a PMF
> profile) was generated from data that have poor sampling in two regions.
>  The contents of profile.xvg look normal.  I don't know which of these
> curves corresponds to histo.xvg, because the histograms therein look fine.
>
> Please make sure to give full descriptions of these files.  You've quote a
> message that is over a month old.  I've replied to hundreds of messages
> since then and I do not remember the full context of our discussion.
>
> -Justin
>
>  On Tue, Jul 5, 2011 at 5:16 PM, Justin A. Lemkul > jalem...@vt.edu>> wrote:
>>
>>
>>
>>shahid nayeem wrote:
>>
>>Dear Justin
>>I did pmf calculation for my protein-protein complex using your
>>tutorial.Off course changing the pull_direction suitable for my
>>protein but more or less following the same strategy. I am using
>>gromacs_4.5.4 and g_wham utility. The profile.xvg file which I
>>get is attached and it shows two dips in PE curve. Please see it
>>and tell me why I am getting these dips.
>>
>>
>>You have insufficient sampling in at least these two regions.  Your
>>histograms should confirm this.
>>
>>-Justin
>>
>>-- ==**__==
>>
>>Justin A. Lemkul
>>Ph.D. Candidate
>>ICTAS Doctoral Scholar
>>MILES-IGERT Trainee
>>Department of Biochemistry
>>Virginia Tech
>>Blacksburg, VA
>>jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
>>
>>
>> http://www.bevanlab.biochem.__**vt.edu/Pages/Personal/justin<http://vt.edu/Pages/Personal/justin>
>>
>> <http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
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>>
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Re: [gmx-users] Arginine_Hydrochloride topology

[shahid nayeem]

Hi Justin
I prepared a box of SOL and arginine Hydrochloride. But when I solvate my
protein with this box now the positively charged arginine is as solvent and
this causes problem in grompp. It gives error like "No such Molecule types
ARG" etc. Solvating arginine with water and preparing a box was without
error. which forcefield in gromacs has inbuilt .itp file for free amino acid
which I can include in my .top file.
Shahid Nayeem

On Fri, Jul 29, 2011 at 5:02 PM, Justin A. Lemkul  wrote:

>
>
> shahid nayeem wrote:
>
>> Dear All I am trying to find the topology and parameterof free Arginine
>> Hydrchloride molecule in gromacs force-field format. Developing it in
>> Pro-Drg will not serve as  I will need some other parametrization tool to
>> check it charges. If someone can help, I will be grateful.
>>
>
> Isn't this just a protonated arginine (normal state for neutral pH) with a
> chloride counterion?  There's nothing special about it, just run a
> coordinate file through pdb2gmx with the force field of your choice.
>
> -Justin
>
> --
> ==**==
>
> 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<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>
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[gmx-users] Adding_topology_aminoacid

[shahid nayeem]

Dear All
I am solvating my protein in a cubical box with a .gro file containing water
and one amino acidX. when I run grompp I get error "No such moleculetype
aminoacidX" . Should I create de novo .itp file for the amino acidX on
proDrg because I tried to include ffbonded.itp and ffnonbonded.itp in .top
file but this also gives error in grompp. Creating a new .itp file on ProDrg
will again cause problem of charge and parametrization. Since it is
individual normal amino acid not present in protein but as insert molecule
in solvation box so I think creating new .itp file should not be needed.
shahid Nayeem
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[gmx-users] Arginine_Hydrochloride topology

[shahid nayeem]

Dear All
I am trying to find the topology and parameterof free Arginine Hydrchloride
molecule in gromacs force-field format. Developing it in Pro-Drg will not
serve as  I will need some other parametrization tool to check it charges.
If someone can help, I will be grateful.
shahid Nayeem
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[gmx-users] pmf_calculation

[shahid nayeem]

Dear Justin
Here is my histogram file which does not show any window overlap. The
sampling window I choose was 0.2 nm which I think is very large. Please
suggest.
Shahid nayeem


hist.xvg
Description: Binary data
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[gmx-users] pmf_calculation

[shahid nayeem]

Dear Justin
I did pmf calculation for my protein-protein complex using your tutorial.Off
course changing the pull_direction suitable for my protein but more or less
following the same strategy. I am using gromacs_4.5.4 and g_wham utility.
The profile.xvg file which I get is attached and it shows two dips in PE
curve. Please see it and tell me why I am getting these dips.
Shahid Nayeem


profile.xvg
Description: Binary data
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[gmx-users] Thermal_Unfolding

[shahid nayeem]

Dear Gromacs Users

I want to study thermal unfolding of protein in gromacs. One way to do is
to simulate at different temperature. What I want to do is to gradually
increase temperature after each n number of steps and collect the n' number
of frame for each temperature interval. If I can do this in gromacs then
what should be the .mdp file for such increment in temperature at regular
intervals.
Thanks for any help.
Shahid Nayeem
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Re: [gmx-users] binding_affinity

[shahid nayeem]

Hi Justin
Before trying for my system I am trying to learn running these
simulation with the help of your tutorial. The only change I made is
that I applied pull_code for 2nm movement only in order to save time.
Thereafter, with trjconv I generated all 200 conf.gro. when I run your
perl script it does gives an oitput of summary_distance.dat. It has
one column of conf.gro number but no distance. Where I am wrong.
Shahid Nayeem

On Tue, Apr 19, 2011 at 6:20 PM, Justin A. Lemkul  wrote:
>
>
> Justin A. Lemkul wrote:
>>
>>
>> shahid nayeem wrote:
>>>
>>> Hi Justin
>>> Thanks a lot. What is the purpose of adding 100mM NaCl. Is it
>>> mimicking physiological condition.
>>
>> More of a hybrid of physiological and in vitro conditions.  Please see the
>> referenced paper for more details.
>>
>
> ...and again, please don't necessarily conclude that just because someone
> did this for a tutorial that you should inherently be doing it for your
> system.  The tutorial is but one example of a workflow, derived from my own
> specific work. Construct a model that is most appropriate to your purposes.
>
> -Justin
>
> --
> 
>
> 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
>
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Re: [gmx-users] binding_affinity

[shahid nayeem]

Hi Justin
Thanks a lot. What is the purpose of adding 100mM NaCl. Is it
mimicking physiological condition.
Shahid Nayeem


On Tue, Apr 19, 2011 at 5:47 PM, Justin A. Lemkul  wrote:
>
>
> shahid nayeem wrote:
>>
>> Hi Justin
>> I went through your tutorial of umbrella sampling. Please clarify that
>> while generating configuration one requires index.ndx of certain
>> residue. These residue are from the restrained chain or from the chain
>> on which pulling force is to be applied in order to separate the
>> chain. why two groups are created. Does index.ndx should contain all
>> residue from the chain which has to move or few are sufficient.
>
> Do what is appropriate for your system.  The reasons for the restraints I
> used are described in my paper that I link from the tutorial.  I certainly
> hope you've read it to understand the methodology.  Thus you do not
> necessarily have to apply the exact methodology to get a sensible result.
>
> You need two groups - a reference group and a group to which the pulling
> force is applied.  Maybe your reference group (whatever it is) needs to be
> restrained to avoid structural deformation, maybe it doesn't.  Whether or
> not an index file is necessary also depends on how you set up the reference
> and pulled groups.  If they are default groups, then you don't need an index
> file, but if they are some subset of existing groups, then yes, you need a
> custom index file, just like any other Gromacs operation.
>
> -Justin
>
>> Shahid Nayeem
>>
>> On Thu, Apr 14, 2011 at 6:34 PM, Justin A. Lemkul  wrote:
>>>
>>> shahid nayeem wrote:
>>>>
>>>> Dear All
>>>> I have some protein complex pdb after docking two monomers. The
>>>> scoring of these docked structure are not true representative of
>>>> binding affinity. I want calculate the binding affinity affinity of
>>>> these docked pdb. Can anyone suggest me, how should I proceed.
>>>> Shahid Nayeem
>>>
>>> Calculating a PMF is a common approach.
>>>
>>> http://www.gromacs.org/Documentation/How-tos/Potential_of_Mean_Force
>>>
>>> -Justin
>>>
>>> --
>>> 
>>>
>>> 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
>>>
>>> 
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>>
>
> --
> 
>
> 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
>
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Re: [gmx-users] binding_affinity

[shahid nayeem]

Hi Justin
I went through your tutorial of umbrella sampling. Please clarify that
while generating configuration one requires index.ndx of certain
residue. These residue are from the restrained chain or from the chain
on which pulling force is to be applied in order to separate the
chain. why two groups are created. Does index.ndx should contain all
residue from the chain which has to move or few are sufficient.
Shahid Nayeem

On Thu, Apr 14, 2011 at 6:34 PM, Justin A. Lemkul  wrote:
>
>
> shahid nayeem wrote:
>>
>> Dear All
>> I have some protein complex pdb after docking two monomers. The
>> scoring of these docked structure are not true representative of
>> binding affinity. I want calculate the binding affinity affinity of
>> these docked pdb. Can anyone suggest me, how should I proceed.
>> Shahid Nayeem
>
> Calculating a PMF is a common approach.
>
> http://www.gromacs.org/Documentation/How-tos/Potential_of_Mean_Force
>
> -Justin
>
> --
> 
>
> 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
>
> 
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[gmx-users] binding_affinity

[shahid nayeem]

Dear All
I have some protein complex pdb after docking two monomers. The
scoring of these docked structure are not true representative of
binding affinity. I want calculate the binding affinity affinity of
these docked pdb. Can anyone suggest me, how should I proceed.
Shahid Nayeem
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Re: [gmx-users] g_rms and g_cluster

[shahid nayeem]

Hi Justin
If I make an index group with backbone and CA C N O group of the
concerned residues and then do least square fitting then do this
fitting is equivalent to backbone fitting first and then translating
to coincide CA of the residue of interest. Is there any other
programme developed for gromacs trajectory analysis where I can do
backbone fitting first and then translate to coincide CA of residue of
interest before calculating RMSD.
Shahid Nayeem

On Thu, Feb 24, 2011 at 7:14 PM, Justin A. Lemkul  wrote:
>
>
> shahid nayeem wrote:
>>
>> Dear All
>>
>> I want to calculate RMSD of one side chain residue from simulation
>> trajectory after full backbone alignment as well as translating to
>> coincide CA of the residue of interest. Is it possible to do with
>> g_rms both backbone alignment as well as translating to coincide CA.
>
> Least-squares fitting is performed on whatever group you choose (i.e.
> backbone), and the calculation group can then be whatever you want.  You can
> use trjconv to do translational fitting, but I don't know that you can force
> g_rms to always align this certain atom and still perform a backbone fit;
> these two may work against one another, even if the difference is small.
>
>> Another clarification is that in gromacs g_cluster how can I use
>> greedy algorithm for clustering.
>
> What is a "greedy" algorithm?  The available methods are described in the
> manual and/or g_cluster -h.
>
> -Justin
>
>> Shahid Nayeem
>
> --
> 
>
> 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
>
> 
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[gmx-users] g_rms and g_cluster

[shahid nayeem]

Dear All

I want to calculate RMSD of one side chain residue from simulation
trajectory after full backbone alignment as well as translating to
coincide CA of the residue of interest. Is it possible to do with
g_rms both backbone alignment as well as translating to coincide CA.
Another clarification is that in gromacs g_cluster how can I use
greedy algorithm for clustering.
Shahid Nayeem
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[gmx-users] backbone_few_sidechain_fixed

[shahid nayeem]

Dear All
My protein complex has three chains A B C. I created three posre.itp
for backbone and some side chain which is not on the interface for
each of the chain. I put these in .top file as follows


;   File 'complex.top' was generated
;   By user: shahid (511)
;   On host: coe.iitd.ac.in
;   At date: Thu Feb 17 17:52:59 2011
;
;   This is your topology file
;   "They Paint Their Faces So Differently From Ours" (Gogol Bordello)
;
; Include forcefield parameters
#include "ffG43a1.itp"

; Include A-chain topologies
#include "complex_A.itp"
#include "complex_B.itp"
#include "complex_C.itp"

#ifdef POSRES
#include "posreA.itp"
#include "posreB.itp"
#include "posreC.itp"
#endif
 If I keep only one posreA.itp then grompp runs without error but if I
use all three or two posre.itp it gives following error.

Program grompp, VERSION 4.0.7
Source code file: toppush.c, line: 1275

Fatal error:
[ file posreB.itp, line 118 ]:
Atom index (968) in position_restraints out of bounds (1-966).
This probably means that you have inserted topology section
"position_restraints"
in a part belonging to a different molecule than you intended to.
In that case move the "position_restraints" section to the right molecule.

I separated including topology and defining posres in three different
parts but even then it gives error and grompp fails. In my posre.itp
generated by genrestr I selected a group containing backbone and some
side chains.
My Idea is to keep the backbone as well as side chain of all the
residues which are not on interface fixed and allow free movement of
only interface residue and then run full MD. For above procedure I
defined define = POSRES in full.mdp
 Please suggest what should I do .
For a single chain I did MD keeping backbone fixed and allowing side
chain free movement. In my posres.itp I used a force of 2000 kj to
keep them in fixed position with option genrestr -fc.
Waiting for reply

Shahid Nayeem
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[gmx-users] server_for_Gaussian

[shahid nayeem]

Dear All

If any one is aware of a server on which one can upload job for
running Gaussian, Please let me know. This I need to modify charges in
 the topology file created by ProDrg server.
Shahid Nayeem
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Re: [gmx-users] solvation_box_preparation

[shahid nayeem]

Hi Justin
Thanks a lot.
I tried doing energy minimization and th lowering emtotal to 200 and
the system converged to
Steepest Descents converged to Fmax < 200 in 1411 steps
Potential Energy  = -3.9063050e+05
Maximum force =  1.3442458e+02 on atom 927
Norm of force =  1.4758101e+01
 For equilibration of solvation box I am following a biophys j paper
in which protocol for urea box preparation is given. A simulated
annealing under high pressure (ref_p=100) to cool system from 300 to
0K thereafter heating back to 300K at ref_p=1. Again 1ns MD at same
condition. If this way is harsh treatment of system then suggest me
the way out.
My sa.mdp sa_hot.mdp and sa_equilibriation.mdp as well as chaps.itp
are attached with this mail
Shahid Nayeem
On Mon, Jan 31, 2011 at 9:47 AM, Justin A. Lemkul  wrote:
>
>
> shahid nayeem wrote:
>>
>> Please tell me where I am wrong. I downloaded pdb of chaps and used
>> prodrg server to get .itp and .gro file. Then I checked .itp for any
>> missing charge and I found it correct. Then I created 6.0x6.0x6.0 box
>
> PRODRG doesn't have a problem of missing charges.  It provides notoriously
> incorrect charges.
>
>> with genbox inserting 7 molecules of chaps.gro. Then again using
>> genbox and -maxsol I put 510 spc.itp in the box to get a density
>> approaching 1. Then I did steepest descent energy minimization with
>> constraints = none, for emtotal=2000 and emstep=3000. Up to this the
>
> These settings make no sense.  An emtol of 2000 is very high, and emstep of
> 3000 is total nonsense.  How well did you EM converge?  What were the values
> of the potential energy and maximum force?
>
>> gromacs runs fine. when I start simulated annealing for cooling at
>> high pressure with constraint = all_bonds the programme gives fatal
>> error linc warning and stops. If I do energy minimization with
>> constraint =all_bonds then also with some error of linc wrning the
>> minimization is completed. When I do minimization without adding water
>> then there is no linc warning and minimization is completed but with
>> final positive potential energy. Then as suggested by Justin I used
>> smaller box and there also in simulated annealing stage the system
>> gives linc warning and the programme stops with fatal error. Please
>> tell me where I am wrong.
>
> How about simplifying the problem.  Does the system run under normal
> conditions?  In other words, can you run normal MD?  You're treating the
> system very harshly with the combination of high pressure and annealing.
>  Without seeing your .mdp file for this process, it's impossible to say how
> reasonable your settings are.
>
> It is also possible that your parameters for CHAPS (if they are the default
> ones from PRODRG) are incorrect.  The charges and charge groups nearly
> always are. Without seeing them, there's nothing better to offer.
>
> -Justin
>
>> shahid nayeem
>>
>> On Fri, Jan 28, 2011 at 10:59 AM, Mark Abraham 
>> wrote:
>>>
>>> On 28/01/2011 3:51 PM, shahid nayeem wrote:
>>>>
>>>> Thanks Justin
>>>> I tried with new box size of 2.8x2.8x2.8 . During energy minimization
>>>> with steepest descent to force of 2000 and constraint=none, the system
>>>> converged in 754 steps with positive potential energy. In subsequent
>>>> simulated annealing with constraint all bonds it starts giving link
>>>> warning in 0 step with rms 7407.805164, max 66989.116545 (between atom
>>>> 94 and 117) and a list of bond thar rotated more than 30 degree almost
>>>> atom number belonging to chaps molecule.
>>>
>>> You've set up a system that isn't stable, but we don't have enough
>>> information to have any idea why. "I tried with new box size" doesn't go
>>> close to describing your method in enough detail for anyone to know where
>>> you went wrong.
>>>
>>> See http://www.gromacs.org/Documentation/Terminology/Blowing_Up for
>>> generic
>>> tips
>>>
>>> Mark
>>>
>>>> Please help.
>>>> shahid Nayeem
>>>>
>>>> On Thu, Jan 27, 2011 at 7:06 PM, Justin A. Lemkul
>>>>  wrote:
>>>>>
>>>>> shahid nayeem wrote:
>>>>>>
>>>>>> Dear All
>>>>>>
>>>>>> I am sending this mail again on user list because my reply to Mark’s
>>>>>> query was not uploaded on the list.
>>>>>>
>>>>>> Original messge:
>>>>>>
>>>>>> I am trying to p

Re: [gmx-users] interface_enrgy

[shahid nayeem]

That means in energy group in .mdp file I should write interface.ndx
and tell me if on interface there is hydrogen bond then its value I
will get or not.
Shahid Nayeem


On Mon, Feb 7, 2011 at 6:50 PM, Justin A. Lemkul  wrote:
>
>
> shahid nayeem wrote:
>>
>> Dear User
>> I am doing MD on protein complex keeping backbone as well as side
>> chain of all residues which is not on th interface fixed. For this I
>> prepared posre_backbone_sidechain.itp and defined this in .top file
>> for full MD. Now I want to know from the trajectory the best side
>> chain conformation of the interface residues for which I want to see
>> the change in total energy of the interface residues throught the
>> trajectory. I prepared index file for interface residues. But g_energy
>> command does not takes -n index.ndx to calculate energy of these
>> groups. How can I do that. Please suggest.
>
> You can set energygrps in the .mdp file and use mdrun -rerun to re-calculate
> the components of the nonbonded interaction energy between different groups.
>  You cannot decompose the total energy or bonded terms.  If you've used PME,
> the long-range term cannot be decomposed, either.
>
> -Justin
>
>> Thanking you
>>
>> Shahid Nayeem
>
> --
> 
>
> 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
>
> 
> --
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[gmx-users] interface_enrgy

[shahid nayeem]

Dear User
I am doing MD on protein complex keeping backbone as well as side
chain of all residues which is not on th interface fixed. For this I
prepared posre_backbone_sidechain.itp and defined this in .top file
for full MD. Now I want to know from the trajectory the best side
chain conformation of the interface residues for which I want to see
the change in total energy of the interface residues throught the
trajectory. I prepared index file for interface residues. But g_energy
command does not takes -n index.ndx to calculate energy of these
groups. How can I do that. Please suggest.
Thanking you

Shahid Nayeem
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Re: [gmx-users] solvation_box_preparation

[shahid nayeem]

Please tell me where I am wrong. I downloaded pdb of chaps and used
prodrg server to get .itp and .gro file. Then I checked .itp for any
missing charge and I found it correct. Then I created 6.0x6.0x6.0 box
with genbox inserting 7 molecules of chaps.gro. Then again using
genbox and -maxsol I put 510 spc.itp in the box to get a density
approaching 1. Then I did steepest descent energy minimization with
constraints = none, for emtotal=2000 and emstep=3000. Up to this the
gromacs runs fine. when I start simulated annealing for cooling at
high pressure with constraint = all_bonds the programme gives fatal
error linc warning and stops. If I do energy minimization with
constraint =all_bonds then also with some error of linc wrning the
minimization is completed. When I do minimization without adding water
then there is no linc warning and minimization is completed but with
final positive potential energy. Then as suggested by Justin I used
smaller box and there also in simulated annealing stage the system
gives linc warning and the programme stops with fatal error. Please
tell me where I am wrong.
shahid nayeem

On Fri, Jan 28, 2011 at 10:59 AM, Mark Abraham  wrote:
> On 28/01/2011 3:51 PM, shahid nayeem wrote:
>>
>> Thanks Justin
>> I tried with new box size of 2.8x2.8x2.8 . During energy minimization
>> with steepest descent to force of 2000 and constraint=none, the system
>> converged in 754 steps with positive potential energy. In subsequent
>> simulated annealing with constraint all bonds it starts giving link
>> warning in 0 step with rms 7407.805164, max 66989.116545 (between atom
>> 94 and 117) and a list of bond thar rotated more than 30 degree almost
>> atom number belonging to chaps molecule.
>
> You've set up a system that isn't stable, but we don't have enough
> information to have any idea why. "I tried with new box size" doesn't go
> close to describing your method in enough detail for anyone to know where
> you went wrong.
>
> See http://www.gromacs.org/Documentation/Terminology/Blowing_Up for generic
> tips
>
> Mark
>
>> Please help.
>> shahid Nayeem
>>
>> On Thu, Jan 27, 2011 at 7:06 PM, Justin A. Lemkul  wrote:
>>>
>>> shahid nayeem wrote:
>>>>
>>>> Dear All
>>>>
>>>> I am sending this mail again on user list because my reply to Mark’s
>>>> query was not uploaded on the list.
>>>>
>>>> Original messge:
>>>>
>>>> I am trying to prepare a solvation box of chaps. After generating .itp
>>>> and .gro at ProDrg and thorough check of charges, I started with a box
>>>> size of 6x6x6. Energy minimization, simulated annealing (Cooling under
>>>> high pressure and again heating at normal pressure) as well as final
>>>> equilibration ran smoothly. But finally I get a box where all water
>>>> molecules get accumulated in two three small region within the box and
>>>> all chaps molecules gets accumulated in another small regions.I wanted
>>>> near random uniform distribution of chaps in water. Any help from
>>>> user, where I am wrong and what should I do.
>>>>
>>>> Reply to query.
>>>>
>>>> I created a box of 6x6x6 inserting 7 molecule of chaps with (genbox
>>>> –ci 7 chaps.gro).Then I solvated the output box  with genbox using
>>>> -maxsol 500 and spc216.gro. On visualization, at this stage itself
>>>> uniform solvation did not occur (I got water in one region and chaps
>>>> molecule in other region) but I observed a similar situation while
>>>
>>> If your box was not completely solvated, then don't use -maxsol.  A box
>>> of
>>> 6x6x6 nm should require more than 500 molecules of water to fill.  If
>>> you're
>>> trying to achieve some specific mole fraction or concentration, then
>>> re-figure your box size.
>>>
>>> -Justin
>>>
>>>> preparing 10M urea salvation box. This was followed by 1ns simulated
>>>> annealing from temp 300K to 0K and pressure 100 bar, then 1ns
>>>> simulated annealing from temp. 0k to 300k and then ins equilibriation
>>>> at this temperature. In case of urea finally I got uniformly solvated
>>>> urea_water_box but in chaps I couldn’t get it.
>>>>
>>>> Shahid Nayeem
>>>
>>> --
>>> 
>>>
>>> Justin A. Lemkul
>>> Ph.D. Candidate
>>> ICTAS Doctoral Scholar
>>> MILES-IGERT Trainee
>>> Department of Biochemistry
>>> Virginia Te

Re: [gmx-users] solvation_box_preparation

[shahid nayeem]

Thanks Justin
I tried with new box size of 2.8x2.8x2.8 . During energy minimization
with steepest descent to force of 2000 and constraint=none, the system
converged in 754 steps with positive potential energy. In subsequent
simulated annealing with constraint all bonds it starts giving link
warning in 0 step with rms 7407.805164, max 66989.116545 (between atom
94 and 117) and a list of bond thar rotated more than 30 degree almost
atom number belonging to chaps molecule.
Please help.
shahid Nayeem

On Thu, Jan 27, 2011 at 7:06 PM, Justin A. Lemkul  wrote:
>
>
> shahid nayeem wrote:
>>
>> Dear All
>>
>> I am sending this mail again on user list because my reply to Mark’s
>> query was not uploaded on the list.
>>
>> Original messge:
>>
>> I am trying to prepare a solvation box of chaps. After generating .itp
>> and .gro at ProDrg and thorough check of charges, I started with a box
>> size of 6x6x6. Energy minimization, simulated annealing (Cooling under
>> high pressure and again heating at normal pressure) as well as final
>> equilibration ran smoothly. But finally I get a box where all water
>> molecules get accumulated in two three small region within the box and
>> all chaps molecules gets accumulated in another small regions.I wanted
>> near random uniform distribution of chaps in water. Any help from
>> user, where I am wrong and what should I do.
>>
>> Reply to query.
>>
>> I created a box of 6x6x6 inserting 7 molecule of chaps with (genbox
>> –ci 7 chaps.gro).Then I solvated the output box  with genbox using
>> -maxsol 500 and spc216.gro. On visualization, at this stage itself
>> uniform solvation did not occur (I got water in one region and chaps
>> molecule in other region) but I observed a similar situation while
>
> If your box was not completely solvated, then don't use -maxsol.  A box of
> 6x6x6 nm should require more than 500 molecules of water to fill.  If you're
> trying to achieve some specific mole fraction or concentration, then
> re-figure your box size.
>
> -Justin
>
>> preparing 10M urea salvation box. This was followed by 1ns simulated
>> annealing from temp 300K to 0K and pressure 100 bar, then 1ns
>> simulated annealing from temp. 0k to 300k and then ins equilibriation
>> at this temperature. In case of urea finally I got uniformly solvated
>> urea_water_box but in chaps I couldn’t get it.
>>
>> Shahid Nayeem
>
> --
> 
>
> 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@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
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[gmx-users] solvation_box_preparation

[shahid nayeem]

Dear All

I am sending this mail again on user list because my reply to Mark’s
query was not uploaded on the list.

Original messge:

I am trying to prepare a solvation box of chaps. After generating .itp
and .gro at ProDrg and thorough check of charges, I started with a box
size of 6x6x6. Energy minimization, simulated annealing (Cooling under
high pressure and again heating at normal pressure) as well as final
equilibration ran smoothly. But finally I get a box where all water
molecules get accumulated in two three small region within the box and
all chaps molecules gets accumulated in another small regions.I wanted
near random uniform distribution of chaps in water. Any help from
user, where I am wrong and what should I do.

Reply to query.

I created a box of 6x6x6 inserting 7 molecule of chaps with (genbox
–ci 7 chaps.gro).Then I solvated the output box  with genbox using
-maxsol 500 and spc216.gro. On visualization, at this stage itself
uniform solvation did not occur (I got water in one region and chaps
molecule in other region) but I observed a similar situation while
preparing 10M urea salvation box. This was followed by 1ns simulated
annealing from temp 300K to 0K and pressure 100 bar, then 1ns
simulated annealing from temp. 0k to 300k and then ins equilibriation
at this temperature. In case of urea finally I got uniformly solvated
urea_water_box but in chaps I couldn’t get it.

Shahid Nayeem
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Re: [gmx-users] solvation_box

[shahid nayeem]

I forgot to mention that when I prepared urea_water box then also I got
similar box of water in one region and urea in other region separated from
it. But on minimization and following simulated annealing
and equilibration I got a uniformly mixed urea water box.
Shahid Nayeem

On Thu, Jan 27, 2011 at 12:30 PM, shahid nayeem  wrote:

> Hi Mark
> Thanks.
> I created a box of 6x6x6 inserting 7 molecule of chaps with genbox.Then I
> solvated this box with genbox using -maxsol 500 and spc216.gro. On
> visualization, at this stage itself uniform solvation did not occur and I
> got water in one region and chaps molecule spread throughout box but not
> inside water. I should have visualized it earlier before going for
> minimization. Please help me.
> shahid Nayeem
>
> On Thu, Jan 27, 2011 at 11:36 AM, Mark Abraham wrote:
>
>>
>>
>> On 01/27/11, *shahid nayeem *  wrote:
>>
>> Dear All
>> I am trying to prepare a solvation box of chaps. After generating .itp and
>> .gro at ProDrg and thorough check of charges, I started with a box size of
>> 6x6x6. Energy minimization, simulated annealing (Cooling under high pressure
>> and again heating at normal pressure) as well as final equilibration ran
>> smoothly. But finally I get a box where all water molecules get accumulated
>> in two three small region within the box and all chaps molecules gets
>> accumulated in another small regions.I wanted near random uniform
>> distribution of chaps in water. Any help from user, where I am wrong and
>> what should I do.
>>
>>
>> You haven't told us how you've solvated the system (e.g. with genbox),
>> that it looked OK when you visualized it between each step, and that you're
>> sure your observations cannot be rationalized as a periodicity artefact.
>>
>> Mark
>> --
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>>
>
>
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Re: [gmx-users] solvation_box

[shahid nayeem]

Hi Mark
Thanks.
I created a box of 6x6x6 inserting 7 molecule of chaps with genbox.Then I
solvated this box with genbox using -maxsol 500 and spc216.gro. On
visualization, at this stage itself uniform solvation did not occur and I
got water in one region and chaps molecule spread throughout box but not
inside water. I should have visualized it earlier before going for
minimization. Please help me.
shahid Nayeem

On Thu, Jan 27, 2011 at 11:36 AM, Mark Abraham wrote:

>
>
> On 01/27/11, *shahid nayeem *  wrote:
>
> Dear All
> I am trying to prepare a solvation box of chaps. After generating .itp and
> .gro at ProDrg and thorough check of charges, I started with a box size of
> 6x6x6. Energy minimization, simulated annealing (Cooling under high pressure
> and again heating at normal pressure) as well as final equilibration ran
> smoothly. But finally I get a box where all water molecules get accumulated
> in two three small region within the box and all chaps molecules gets
> accumulated in another small regions.I wanted near random uniform
> distribution of chaps in water. Any help from user, where I am wrong and
> what should I do.
>
>
> You haven't told us how you've solvated the system (e.g. with genbox), that
> it looked OK when you visualized it between each step, and that you're sure
> your observations cannot be rationalized as a periodicity artefact.
>
> Mark
> --
> gmx-users mailing listgmx-users@gromacs.org
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>
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[gmx-users] solvation_box

[shahid nayeem]

Dear All
I am trying to prepare a solvation box of chaps. After generating .itp and
.gro at ProDrg and thorough check of charges, I started with a box size of
6x6x6. Energy minimization, simulated annealing (Cooling under high pressure
and again heating at normal pressure) as well as final equilibration ran
smoothly. But finally I get a box where all water molecules get accumulated
in two three small region within the box and all chaps molecules gets
accumulated in another small regions.I wanted near random uniform
distribution of chaps in water. Any help from user, where I am wrong and
what should I do.
Shahid nayeem
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[gmx-users] preparation_solvation_box

[shahid nayeem]

Dear Gmx User
I want to prepare a solvation box for say 50mM chaps solution. The density
is not known. How should I start calculating the number of chaps molecule
and number of water molecule required for say 6X6X6 size box, which after
equilibriation should give the exact strength of the solution. For Urea and
guanidinium I know the references and mail archive has many suggestion but
how I should proceed with this new solvation box.

msnayeem
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[gmx-users] Interaction_between_protein_small_molecule

[shahid nayeem]

Dear Gromacs Users

I wanted to study the interaction between a small molecule and protein. I
prepared the system by inserting small molecule -nmol and protein by genbox
and then I solvated it with water. when I tried to do PR dynamics it started
giving many LINC WARNINGS. I reduced the time of equilibration and then PR
run was completed without any warning. When I used production run it started
giving LINC warning.Even after setting GMX_MAXCONSTRWARN to -1 I am getting
LINC warning and programme termination with fatal error. Instead of simple
docking I want to do MD with GROMACS to see interaction between the two
molecule. Please suggest me, how can I do this.
Thanking you.

Shahid Nayeem
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[gmx-users] Terminal_ARG_residue causing problem in pdb2gmx

[shahid nayeem]

Dear Gromacs User
My pdb is homodimer with  Arg as c-terminal residue. With this pdb I am
etting following error in pdb2gmx command
Program pdb2gmx, VERSION 4.0.7
Source code file: pdb2gmx.c, line: 429

Fatal error:
Atom OXT in residue ARG 107 not found in rtp entry with 17 atoms
 while sorting atoms

The command executed is as follows
 pdb2gmx   -f.pdb   -o.gro   -p  .top

I tried to change the OXT atom name in pdb file to O2, then also I am
getting the same error.
In .rtp entry there is ARG residue as N-ter  but for C-ter ARG there is no
residue.
Please suggest.
Waiting for  helps from gromacs users.
Shahid Nayem
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Re: [gmx-users] heme

[shahid nayeem]

Hi Erik
I am using ffG43a1 force field. It has heme topology. But in Cyt C. FE is
bonded to both NR of HIS and SD of MET. The parameter for the bond, FE SD,
 angles e.g. NR (HIS) FE SD(MET)  and dihedral  angle CH2(MET)  SD (MET) FE
NR(HIS) is missing in this force field. hence I am getting error while
running grompp. Please suggest me what should I do.
Shahid Nayeem

On Thu, Nov 25, 2010 at 3:12 AM, Erik Marklund  wrote:

> shahid nayeem skrev 2010-11-24 18.02:
>
>  Dear all
>> I am trying MD of cyt C containing heme. I am able to generate bonds with
>> specbond.dat by pdb2gmx. After using editconf and genbox, when I tried
>> grompp I got error about unrecognized bonds/angles. I made bond with MET SD
>> and FE of Heme. As earlier suggested on this list I wrote to get parameter
>> for these bonds but I couldnt get it. If someone on this mailing list can
>> help me I will be grateful. Cyt C is very widely modelled protein with
>> Gomacs in literature hence I expect to get some help from the forum.
>> shahid nayeem
>>
> A long time ago I simulated CytC with one of the gromos force fields. It
> worked right out of the box. What forcefield are you using?
>
> --
> ---
> Erik Marklund, PhD student
> Dept. of Cell and Molecular Biology, Uppsala University.
> Husargatan 3, Box 596,75124 Uppsala, Sweden
> phone:+46 18 471 4537fax: +46 18 511 755
> er...@xray.bmc.uu.sehttp://folding.bmc.uu.se/
>
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Re: [gmx-users] heme

[shahid nayeem]

I am using ffG43a1 forcefield. its .rtp file contains topology of Heme but
Met SD and FE bond is not there.
Shahid Nayeem

On Thu, Nov 25, 2010 at 5:11 AM, Justin A. Lemkul  wrote:

>
>
> Erik Marklund wrote:
>
>> shahid nayeem skrev 2010-11-24 18.02:
>>
>>> Dear all
>>> I am trying MD of cyt C containing heme. I am able to generate bonds with
>>> specbond.dat by pdb2gmx. After using editconf and genbox, when I tried
>>> grompp I got error about unrecognized bonds/angles. I made bond with MET SD
>>> and FE of Heme. As earlier suggested on this list I wrote to get parameter
>>> for these bonds but I couldnt get it. If someone on this mailing list can
>>> help me I will be grateful. Cyt C is very widely modelled protein with
>>> Gomacs in literature hence I expect to get some help from the forum.
>>> shahid nayeem
>>>
>> A long time ago I simulated CytC with one of the gromos force fields. It
>> worked right out of the box. What forcefield are you using?
>>
>>
> The same problem is frequently reported.  The inter-residue bonds and
> angles are not assigned in pdb2gmx, nor are they present in the force field,
> IIRC.  Hence the fatal errors.  Perhaps something has changed since "a long
> time ago," but I am sure problems exist in recent versions.
>
> -Justin
>
> --
> 
>
> 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
>
> 
>
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[gmx-users] heme

[shahid nayeem]

Dear all
I am trying MD of cyt C containing heme. I am able to generate bonds with
specbond.dat by pdb2gmx. After using editconf and genbox, when I tried
grompp I got error about unrecognized bonds/angles. I made bond with MET SD
and FE of Heme. As earlier suggested on this list I wrote to get parameter
for these bonds but I couldnt get it. If someone on this mailing list can
help me I will be grateful. Cyt C is very widely modelled protein with
Gomacs in literature hence I expect to get some help from the forum.
shahid nayeem
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[gmx-users] following_change_native_contact

[shahid nayeem]

Dear All
How can I follow the changes in native contacts of protein unfolding
trajectory. Is it g_mdmat, if so then how to analyze the results obtained
from this command.
Shahid Nayeem
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[gmx-users] Heme_Grompp_error

[shahid nayeem]

Dear All
I used the following command sequentially to prepare file for energy
minimization and subsequent MD run.
1. pdb2gmx  -f *.pdb -o seq.gro -p seq.top
2. editconf -f seq.gro -o seq_box.gro -d 1.0 -bt cubic
3. genbox   -cp seq_box.gro -cs spc216.gro -o seq_b4ion.gro -p seq.top
4. grompp   -c seq_b4ion.gro -p seq.top -o seq_b4ion.tpr -f em.mdp
grompp gives following error.processing topology...
Opening library file /usr/local/gromacs/share/gromacs/top/ffG43a1.itp
Opening library file /usr/local/gromacs/share/gromacs/top/ffG43a1nb.itp
Opening library file /usr/local/gromacs/share/gromacs/top/ffG43a1bon.itp
Opening library file /usr/local/gromacs/share/gromacs/top/ff_dum.itp
Generated 279 of the 1225 non-bonded parameter combinations

ERROR 1 [file seq.top, line 1965]:
 No default G96Bond types


ERROR 2 [file seq.top, line 5271]:
 No default G96Angle types


ERROR 3 [file seq.top, line 5272]:
 No default G96Angle types


ERROR 4 [file seq.top, line 5648]:
 No default G96Angle types


ERROR 5 [file seq.top, line 5653]:
 No default G96Angle types


ERROR 6 [file seq.top, line 5654]:
 No default G96Angle types


ERROR 7 [file seq.top, line 5655]:
 No default G96Angle types


ERROR 8 [file seq.top, line 5656]:
 No default G96Angle types


ERROR 9 [file seq.top, line 6201]:
 No default Proper Dih. types

Opening library file /usr/local/gromacs/share/gromacs/top/spc.itp
Opening library file /usr/local/gromacs/share/gromacs/top/ions.itp
Excluding 3 bonded neighbours molecule type 'Protein_A'
Excluding 2 bonded neighbours molecule type 'SOL'
Excluding 2 bonded neighbours molecule type 'SOL'

NOTE 1 [file seq.top, line 6932]:
 System has non-zero total charge: 7.01e+00



processing coordinates...
double-checking input for internal consistency...
renumbering atomtypes...
converting bonded parameters...

There was 1 note

---
Program grompp, VERSION 4.0.7
Source code file: grompp.c, line: 986

Fatal error:
There were 9 errors in input file(s)
---
 pdb2gmx works properly using ff43a1 forcefield. My protein contains
Heme.  This heme is bonded to MET SD and NE2 HIS as well as NA NB NC ND of
heme porphyrins. It is actually these six bond which is created in topology
file with pdb2gmx using specbond.dat, giving error in grompp. I tried to
find these bonds in in built files of gromacs i.e. /share/top/ but I
couldnt. Can any one help me and tell me where can I find these bonds/angle
parameters and what should I add in ffG43a1 .itp .rtp files
please help.
Shahid Nayeem
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[gmx-users] Heme_Grompp_error

[shahid nayeem]

Dear All
I used the following command sequentially to prepare file for energy
minimization and subsequent MD run.
1. pdb2gmx  -f *.pdb -o seq.gro -p seq.top
2. editconf -f seq.gro -o seq_box.gro -d 1.0 -bt cubic
3. genbox   -cp seq_box.gro -cs spc216.gro -o seq_b4ion.gro -p seq.top
4. grompp   -c seq_b4ion.gro -p seq.top -o seq_b4ion.tpr -f em.mdp
grompp gives following error.processing topology...
Opening library file /usr/local/gromacs/share/gromacs/top/ffG43a1.itp
Opening library file /usr/local/gromacs/share/gromacs/top/ffG43a1nb.itp
Opening library file /usr/local/gromacs/share/gromacs/top/ffG43a1bon.itp
Opening library file /usr/local/gromacs/share/gromacs/top/ff_dum.itp
Generated 279 of the 1225 non-bonded parameter combinations

ERROR 1 [file seq.top, line 1965]:
 No default G96Bond types


ERROR 2 [file seq.top, line 5271]:
 No default G96Angle types


ERROR 3 [file seq.top, line 5272]:
 No default G96Angle types


ERROR 4 [file seq.top, line 5648]:
 No default G96Angle types


ERROR 5 [file seq.top, line 5653]:
 No default G96Angle types


ERROR 6 [file seq.top, line 5654]:
 No default G96Angle types


ERROR 7 [file seq.top, line 5655]:
 No default G96Angle types


ERROR 8 [file seq.top, line 5656]:
 No default G96Angle types


ERROR 9 [file seq.top, line 6201]:
 No default Proper Dih. types

Opening library file /usr/local/gromacs/share/gromacs/top/spc.itp
Opening library file /usr/local/gromacs/share/gromacs/top/ions.itp
Excluding 3 bonded neighbours molecule type 'Protein_A'
Excluding 2 bonded neighbours molecule type 'SOL'
Excluding 2 bonded neighbours molecule type 'SOL'

NOTE 1 [file seq.top, line 6932]:
 System has non-zero total charge: 7.01e+00



processing coordinates...
double-checking input for internal consistency...
renumbering atomtypes...
converting bonded parameters...

There was 1 note

---
Program grompp, VERSION 4.0.7
Source code file: grompp.c, line: 986

Fatal error:
There were 9 errors in input file(s)
---
 pdb2gmx works properly using ff43a1 forcefield. My protein contains
Heme.  This heme is bonded to MET SD and NE2 HIS as well as NA NB NC ND of
heme porphyrins. It is actually these six bond which is created in topology
file with pdb2gmx using specbond.dat, giving error in grompp. I tried to
find these bonds in in built files of gromacs i.e. /share/top/ but I
couldnt. Can any one help me and tell me where can I find these bonds/angle
parameters and what should I add in ffG43a1 .itp .rtp files
please help.
Shahid Nayeem
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[gmx-users] Heme_Grompp Error

[shahid nayeem]

Dear All
I used the following command sequentially to prepare file for energy
minimization and subsequent MD run.
1. pdb2gmx  -f *.pdb -o seq.gro -p seq.top
2. editconf -f seq.gro -o seq_box.gro -d 1.0 -bt cubic
3. genbox   -cp seq_box.gro -cs spc216.gro -o seq_b4ion.gro -p seq.top
4. grompp   -c seq_b4ion.gro -p seq.top -o seq_b4ion.tpr -f em.mdp
grompp gives following error.processing topology...
Opening library file /usr/local/gromacs/share/gromacs/top/ffG43a1.itp
Opening library file /usr/local/gromacs/share/gromacs/top/ffG43a1nb.itp
Opening library file /usr/local/gromacs/share/gromacs/top/ffG43a1bon.itp
Opening library file /usr/local/gromacs/share/gromacs/top/ff_dum.itp
Generated 279 of the 1225 non-bonded parameter combinations

ERROR 1 [file seq.top, line 1965]:
 No default G96Bond types


ERROR 2 [file seq.top, line 5271]:
 No default G96Angle types


ERROR 3 [file seq.top, line 5272]:
 No default G96Angle types


ERROR 4 [file seq.top, line 5648]:
 No default G96Angle types


ERROR 5 [file seq.top, line 5653]:
 No default G96Angle types


ERROR 6 [file seq.top, line 5654]:
 No default G96Angle types


ERROR 7 [file seq.top, line 5655]:
 No default G96Angle types


ERROR 8 [file seq.top, line 5656]:
 No default G96Angle types


ERROR 9 [file seq.top, line 6201]:
 No default Proper Dih. types

Opening library file /usr/local/gromacs/share/gromacs/top/spc.itp
Opening library file /usr/local/gromacs/share/gromacs/top/ions.itp
Excluding 3 bonded neighbours molecule type 'Protein_A'
Excluding 2 bonded neighbours molecule type 'SOL'
Excluding 2 bonded neighbours molecule type 'SOL'

NOTE 1 [file seq.top, line 6932]:
 System has non-zero total charge: 7.01e+00



processing coordinates...
double-checking input for internal consistency...
renumbering atomtypes...
converting bonded parameters...

There was 1 note

---
Program grompp, VERSION 4.0.7
Source code file: grompp.c, line: 986

Fatal error:
There were 9 errors in input file(s)
---
 pdb2gmx works properly using ff43a1 forcefield. My protein contains
Heme.  This heme is bonded to MET SD and NE2 HIS as well as NA NB NC ND of
heme porphyrins. It is actually these six bond which is created in topology
file with pdb2gmx using specbond.dat, giving error in grompp. I tried to
find these bonds in in built files of gromacs i.e. /share/top/ but I
couldnt. Can any one help me and tell me where can I find these bonds/angle
parameters and what should I add in ffG43a1 .itp .rtp files
please help.
Shahid Nayeem
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Re: [gmx-users] Grompp error: No default g96angle type

[shahid nayeem]

HI
I am using Cytochrome-C  pdb 1hrc.pdb. In pdb2gmx it does not gives
any eror using ffG43a1. .top file produced shows all bonds (Fe & SD of
MET 80 and Fe & NE2 of HIS 18) using spec.dat file but all the error
lines does not have bond/angle nomenclature such as
  809   810 2gb_30
  810   811 2gb_29
  810  1068 2
  812   813 2gb_4
  812   814 2gb_9
  814   815 2gb_2
810 atom SD of MET80 and 1068 is Fe of Heme. I tried modifying .rtp
file of force-field and adding these bonds and giving some name to it
but got the same error in grompp.
Though .top file shows these bonds the .gro file generated does not
show these bonds in VMD while original pdb file shows these bonds.
thanking you.
waiting for your suggestion.
shahid Nayeem


On 7/15/10, Justin A. Lemkul  wrote:
>
>
> shahid nayeem wrote:
>> Hi Justin
>> These errors are from bond between MET/HIS residue and Heme group of
>> my protein. I checked for all these nine errors of bond and angle in
>> th file ffG43a1bon.itp and I couldnt find these defined  in this file.
>>  Using other options of force field also gives error at some point.
>> waiting for your suggestion to proceed further.
>
> One of the most important choices when conducting MD simulations is the
> force
> field.  You'll have to find one that works.  It appears that (unfortunately)
> the
> Gromos force fields do not work out of the box when heme is involved.
>
> If you want specific advice about other force fields, you'll have to
> describe
> your problem much better than "gives error at some point."  No one can help
> you
> sort that out.  You'd do well to look into the literature.  Simulations of
> heme
> proteins are not novel, so clearly others have made this work, and in some
> cases, parameters might be provided for the terms that are missing.
>
> -Justin
>
>> shahid Nayeem
>>
>> On 7/15/10, Justin A. Lemkul  wrote:
>>>
>>> shahid nayeem wrote:
>>>> Dear All
>>>> I used the following command sequentially to prepare file for energy
>>>> minimization and subsequent MD run.
>>>> 1. pdb2gmx  -f *.pdb -o seq.gro -p seq.top
>>>> 2. editconf -f seq.gro -o seq_box.gro -d 1.0 -bt cubic
>>>> 3. genbox   -cp seq_box.gro -cs spc216.gro -o seq_b4ion.gro -p seq.top
>>>> 4. grompp   -c seq_b4ion.gro -p seq.top -o seq_b4ion.tpr -f em.mdp
>>>> grompp gives following error.processing topology...
>>>> Opening library file /usr/local/gromacs/share/gromacs/top/ffG43a1.itp
>>>> Opening library file /usr/local/gromacs/share/gromacs/top/ffG43a1nb.itp
>>>> Opening library file /usr/local/gromacs/share/gromacs/top/ffG43a1bon.itp
>>>> Opening library file /usr/local/gromacs/share/gromacs/top/ff_dum.itp
>>>> Generated 279 of the 1225 non-bonded parameter combinations
>>>>
>>>> ERROR 1 [file seq.top, line 1965]:
>>>>   No default G96Bond types
>>>>
>>>>
>>>> ERROR 2 [file seq.top, line 5271]:
>>>>   No default G96Angle types
>>>>
>>>>
>>>> ERROR 3 [file seq.top, line 5272]:
>>>>   No default G96Angle types
>>>>
>>>>
>>>> ERROR 4 [file seq.top, line 5648]:
>>>>   No default G96Angle types
>>>>
>>>>
>>>> ERROR 5 [file seq.top, line 5653]:
>>>>   No default G96Angle types
>>>>
>>>>
>>>> ERROR 6 [file seq.top, line 5654]:
>>>>   No default G96Angle types
>>>>
>>>>
>>>> ERROR 7 [file seq.top, line 5655]:
>>>>   No default G96Angle types
>>>>
>>>>
>>>> ERROR 8 [file seq.top, line 5656]:
>>>>   No default G96Angle types
>>>>
>>>>
>>>> ERROR 9 [file seq.top, line 6201]:
>>>>   No default Proper Dih. types
>>>>
>>>> Opening library file /usr/local/gromacs/share/gromacs/top/spc.itp
>>>> Opening library file /usr/local/gromacs/share/gromacs/top/ions.itp
>>>> Excluding 3 bonded neighbours molecule type 'Protein_A'
>>>> Excluding 2 bonded neighbours molecule type 'SOL'
>>>> Excluding 2 bonded neighbours molecule type 'SOL'
>>>>
>>>> NOTE 1 [file seq.top, line 6932]:
>>>>   System has non-zero total charge: 7.01e+00
>>>>
>>>>
>>>>
>>>> processing coordinates...
>>>> double-checking input for internal consistency...
>>>> renumbering atomtypes...

Re: [gmx-users] Grompp error: No default g96angle type

[shahid nayeem]

Hi Justin
These errors are from bond between MET/HIS residue and Heme group of
my protein. I checked for all these nine errors of bond and angle in
th file ffG43a1bon.itp and I couldnt find these defined  in this file.
 Using other options of force field also gives error at some point.
waiting for your suggestion to proceed further.
shahid Nayeem

On 7/15/10, Justin A. Lemkul  wrote:
>
>
> shahid nayeem wrote:
>> Dear All
>> I used the following command sequentially to prepare file for energy
>> minimization and subsequent MD run.
>> 1. pdb2gmx  -f *.pdb -o seq.gro -p seq.top
>> 2. editconf -f seq.gro -o seq_box.gro -d 1.0 -bt cubic
>> 3. genbox   -cp seq_box.gro -cs spc216.gro -o seq_b4ion.gro -p seq.top
>> 4. grompp   -c seq_b4ion.gro -p seq.top -o seq_b4ion.tpr -f em.mdp
>> grompp gives following error.processing topology...
>> Opening library file /usr/local/gromacs/share/gromacs/top/ffG43a1.itp
>> Opening library file /usr/local/gromacs/share/gromacs/top/ffG43a1nb.itp
>> Opening library file /usr/local/gromacs/share/gromacs/top/ffG43a1bon.itp
>> Opening library file /usr/local/gromacs/share/gromacs/top/ff_dum.itp
>> Generated 279 of the 1225 non-bonded parameter combinations
>>
>> ERROR 1 [file seq.top, line 1965]:
>>   No default G96Bond types
>>
>>
>> ERROR 2 [file seq.top, line 5271]:
>>   No default G96Angle types
>>
>>
>> ERROR 3 [file seq.top, line 5272]:
>>   No default G96Angle types
>>
>>
>> ERROR 4 [file seq.top, line 5648]:
>>   No default G96Angle types
>>
>>
>> ERROR 5 [file seq.top, line 5653]:
>>   No default G96Angle types
>>
>>
>> ERROR 6 [file seq.top, line 5654]:
>>   No default G96Angle types
>>
>>
>> ERROR 7 [file seq.top, line 5655]:
>>   No default G96Angle types
>>
>>
>> ERROR 8 [file seq.top, line 5656]:
>>   No default G96Angle types
>>
>>
>> ERROR 9 [file seq.top, line 6201]:
>>   No default Proper Dih. types
>>
>> Opening library file /usr/local/gromacs/share/gromacs/top/spc.itp
>> Opening library file /usr/local/gromacs/share/gromacs/top/ions.itp
>> Excluding 3 bonded neighbours molecule type 'Protein_A'
>> Excluding 2 bonded neighbours molecule type 'SOL'
>> Excluding 2 bonded neighbours molecule type 'SOL'
>>
>> NOTE 1 [file seq.top, line 6932]:
>>   System has non-zero total charge: 7.01e+00
>>
>>
>>
>> processing coordinates...
>> double-checking input for internal consistency...
>> renumbering atomtypes...
>> converting bonded parameters...
>>
>> There was 1 note
>>
>> ---
>> Program grompp, VERSION 4.0.7
>> Source code file: grompp.c, line: 986
>>
>> Fatal error:
>> There were 9 errors in input file(s)
>> ---
>>   pdb2gmx works properly using ff43a1 forcefield. My protein contains
>> Heme. I was having N-terminal ACE group which I simply deleted from
>> the pdb.
>> Am I right in deleting this group. How should I proceed to get rid of
>> this error.
>>
>
> That seems like a particularly poor solution.  Simply getting rid of an
> inconvenient group does not sound appropriate.  Ask yourself whether or not
> there is some functionally significant reason to having the ACE group there
> (chain truncation? artificial modification?) and decide.
>
> As for the errors, look into the topology to see which atoms are causing the
> problems.  Then decide if there are indeed appropriate parameters in the
> force
> field for this task.
>
> -Justin
>
>> Thanks in anticipation of help.
>> Shahid Nayeem
>
> --
> 
>
> 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
>
> 
> --
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[gmx-users] Grompp error: No default g96angle type

[shahid nayeem]

Dear All
I used the following command sequentially to prepare file for energy
minimization and subsequent MD run.
1. pdb2gmx  -f *.pdb -o seq.gro -p seq.top
2. editconf -f seq.gro -o seq_box.gro -d 1.0 -bt cubic
3. genbox   -cp seq_box.gro -cs spc216.gro -o seq_b4ion.gro -p seq.top
4. grompp   -c seq_b4ion.gro -p seq.top -o seq_b4ion.tpr -f em.mdp
grompp gives following error.processing topology...
Opening library file /usr/local/gromacs/share/gromacs/top/ffG43a1.itp
Opening library file /usr/local/gromacs/share/gromacs/top/ffG43a1nb.itp
Opening library file /usr/local/gromacs/share/gromacs/top/ffG43a1bon.itp
Opening library file /usr/local/gromacs/share/gromacs/top/ff_dum.itp
Generated 279 of the 1225 non-bonded parameter combinations

ERROR 1 [file seq.top, line 1965]:
  No default G96Bond types


ERROR 2 [file seq.top, line 5271]:
  No default G96Angle types


ERROR 3 [file seq.top, line 5272]:
  No default G96Angle types


ERROR 4 [file seq.top, line 5648]:
  No default G96Angle types


ERROR 5 [file seq.top, line 5653]:
  No default G96Angle types


ERROR 6 [file seq.top, line 5654]:
  No default G96Angle types


ERROR 7 [file seq.top, line 5655]:
  No default G96Angle types


ERROR 8 [file seq.top, line 5656]:
  No default G96Angle types


ERROR 9 [file seq.top, line 6201]:
  No default Proper Dih. types

Opening library file /usr/local/gromacs/share/gromacs/top/spc.itp
Opening library file /usr/local/gromacs/share/gromacs/top/ions.itp
Excluding 3 bonded neighbours molecule type 'Protein_A'
Excluding 2 bonded neighbours molecule type 'SOL'
Excluding 2 bonded neighbours molecule type 'SOL'

NOTE 1 [file seq.top, line 6932]:
  System has non-zero total charge: 7.01e+00



processing coordinates...
double-checking input for internal consistency...
renumbering atomtypes...
converting bonded parameters...

There was 1 note

---
Program grompp, VERSION 4.0.7
Source code file: grompp.c, line: 986

Fatal error:
There were 9 errors in input file(s)
---
  pdb2gmx works properly using ff43a1 forcefield. My protein contains
Heme. I was having N-terminal ACE group which I simply deleted from
the pdb.
Am I right in deleting this group. How should I proceed to get rid of
this error.

Thanks in anticipation of help.
Shahid Nayeem
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[gmx-users] g_sas

[shahid nayeem]

Dear All
Using g_sas on trajectory file with command
g_sas -f .xtc -s .tpr -oa atomarea.xvg
gives following output
   @title "Area per atom"  @xaxis  label "Atom #"  @yaxis  label
"Area (nm\S2\N)" @TYPE xy   1 0.139885 0.0351154  2 0.0510893 0.0236223  3
0.0510077 0.0234374  4 0.0512037 0.0234554  5 0.0284763 0.0401088  6
0.236609 0.108979
Tghe first column is atom no. and what are the values in two columns. I want
average solvent accessible surface area of each atom of my protein in whole
trajectory.
Shahid Nayeem
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Re: [gmx-users] do_dssp

[shahid nayeem]

Hi
No i dont have any capping group
shahid Nayeem


On 5/24/10, Justin A. Lemkul  wrote:
>
>
>
> shahid nayeem wrote:
>
>> Hi Justin
>> I choose group 5 main chain for dssp calculation
>>
>
> Do you have any capping groups (N-acetyl, C-amine, etc)?
>
> -Justin
>
> Shahid Nayeem
>>
>>
>>  On 5/24/10, *Justin A. Lemkul* mailto:jalem...@vt.edu>>
>> wrote:
>>
>>
>>
>>shahid nayeem wrote:
>>
>>Dear All
>>I did 10ns simulation of three peptide residue solvated in
>>water. Each peptide residue is 26 residue long. In final .gro
>>file it is showing total 78 residue which is O.K. as 3x26=78.
>>For inserting three similar peptide I used genconf command. when
>>I run dssp I get total residue as 80. The command for dssp is
>>do_dssp -f  .xtc -s .tpr -o ss.xpm -sc scount.xvg. Part of the
>>output of dssp run is as follows.
>>
>>
>>When prompted, what group did you choose for the analysis?
>>
>>-Justin
>>
>>
>>@ s0 legend "Structure"
>>
>>
>>@ s1 legend "Coil"
>>
>>
>>@ s2 legend "B-Sheet"
>>
>>
>>@ s3 legend "B-Bridge"
>>
>>
>>@ s4 legend "Bend"
>>
>>
>>@ s5 legend "Turn"
>>
>>
>>@ s6 legend "A-Helix"
>>
>>
>>@ s7 legend "5-Helix"
>>
>>
>>@ s8 legend "3-Helix"
>>
>>
>>  04624 0 0 71036 0 3
>>
>> 103926 0 015 435 0 0
>>
>> 203729 0 011 433 0 3
>>
>>     30    37    32 0 011 235 0 0
>>
>> 403631 0 010 630 0 3
>>
>> 504130 0 0 91031 0 0
>>
>>Please suggest why I am not getting the actual number of residue
>>in dssp file.
>>When I follow the same procedure for full protein molecule
>>simulation I get the same number of residue in dssp output as
>>well as final.gro file
>>shahid nayeem
>>
>>
>>-- 
>>
>>Justin A. Lemkul
>>Ph.D. Candidate
>>ICTAS Doctoral Scholar
>>MILES-IGERT Trainee
>>Department of Biochemistry
>>Virginia Tech
>>Blacksburg, VA
>>jalemkul[at]vt.edu <http://vt.edu/> | (540) 231-9080
>>http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>
>>
>>-- gmx-users mailing listgmx-users@gromacs.org
>><mailto:gmx-users@gromacs.org>
>>http://lists.gromacs.org/mailman/listinfo/gmx-users
>>Please search the archive at http://www.gromacs.org/search before
>>posting!
>>Please don't post (un)subscribe requests to the list. Use the www
>>interface or send it to gmx-users-requ...@gromacs.org
>><mailto:gmx-users-requ...@gromacs.org>.
>>Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>>
>>
>>
> --
> 
>
> 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 listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
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Re: [gmx-users] do_dssp

[shahid nayeem]

Hi Justin
I choose group 5 main chain for dssp calculation
Shahid Nayeem


On 5/24/10, Justin A. Lemkul  wrote:
>
>
>
> shahid nayeem wrote:
>
>> Dear All
>> I did 10ns simulation of three peptide residue solvated in water. Each
>> peptide residue is 26 residue long. In final .gro file it is showing total
>> 78 residue which is O.K. as 3x26=78. For inserting three similar peptide I
>> used genconf command. when I run dssp I get total residue as 80. The command
>> for dssp is do_dssp -f  .xtc -s .tpr -o ss.xpm -sc scount.xvg. Part of the
>> output of dssp run is as follows.
>>
>
> When prompted, what group did you choose for the analysis?
>
> -Justin
>
>
>> @ s0 legend "Structure"
>>
>>
>>
>> @ s1 legend "Coil"
>>
>>
>>
>> @ s2 legend "B-Sheet"
>>
>>
>>
>> @ s3 legend "B-Bridge"
>>
>>
>>
>> @ s4 legend "Bend"
>>
>>
>>
>> @ s5 legend "Turn"
>>
>>
>>
>> @ s6 legend "A-Helix"
>>
>>
>>
>> @ s7 legend "5-Helix"
>>
>>
>>
>> @ s8 legend "3-Helix"
>>
>>
>>
>>   04624 0 0 71036 0 3
>>
>>  103926 0 015 435 0 0
>>
>>  203729 0 011 433 0 3
>>
>>  30    37    32 0 011 235 0 0
>>
>>  403631 0 010 630 0 3
>>
>>  504130 0 0 91031 0 0
>>
>> Please suggest why I am not getting the actual number of residue in dssp
>> file.
>> When I follow the same procedure for full protein molecule simulation I
>> get the same number of residue in dssp output as well as final.gro file
>> shahid nayeem
>>
>
> --
> 
>
> 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 listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the www interface
> or send it to gmx-users-requ...@gromacs.org.
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[gmx-users] do_dssp

[shahid nayeem]

Dear All
I did 10ns simulation of three peptide residue solvated in water. Each
peptide residue is 26 residue long. In final .gro file it is showing total
78 residue which is O.K. as 3x26=78. For inserting three similar peptide I
used genconf command. when I run dssp I get total residue as 80. The command
for dssp is do_dssp -f  .xtc -s .tpr -o ss.xpm -sc scount.xvg. Part of the
output of dssp run is as follows.

@ s0 legend "Structure"

@ s1 legend "Coil"

@ s2 legend "B-Sheet"

@ s3 legend "B-Bridge"

@ s4 legend "Bend"

@ s5 legend "Turn"

@ s6 legend "A-Helix"

@ s7 legend "5-Helix"

@ s8 legend "3-Helix"

   04624 0 0 71036 0 3

  103926 0 015 435 0 0

  203729 0 011 433 0 3

  303732 0 011 235 0 0

  403631 0 010 630 0 3

  504130 0 0 91031 0 0
Please suggest why I am not getting the actual number of residue in dssp
file.
When I follow the same procedure for full protein molecule simulation I get
the same number of residue in dssp output as well as final.gro file
shahid nayeem
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Re: [gmx-users] DSSP

[shahid nayeem]

Hi
When I run  dssp alone with a .pdb file it works well. But when I run with
Gromacs as do_dssp it gives segmentation fault and does not do any
calculation except giving some intermediate files as follows.

Opening library file /usr/local/gromacs/share/gromacs/top/ss.map
Reading frame   0 time0.000
Warning: if there are broken molecules in the trajectory file,
 they can not be made whole without a run input file


Back Off! I just backed up dd8G1JXX to ./#dd8G1JXX.1#
Segmentation fault

shahid


On 5/18/10, Justin A. Lemkul  wrote:
>
>
>
> shahid nayeem wrote:
>
>> Hi
>> After posting this mail I did some google search and after changing the
>> executible name to dssp I moved it in /usr/local/bin/ After this when I did
>> do_dssp it starts running asks to select a group I choose main chain 5, then
>> it generates some intermediate file and gives error as segmentation fault. I
>> though this problem was because of the executible in /usr/local/bin/ and
>> rest of file in another directory say /home/shahid/software/dssp/. For this
>> first I set the path in ~/.bascrc
>>
>
> Other files should be irrelevant.  The only file you need is the dssp
> binary.
>
> as DSSP=/home/shahid/software/dssp/DsspCmbi. I tried to run do_dssp I got
>> the same intermediate file generated backing up the previous one.
>>
>
> Intermediate files are not an issue.  When the executable is in this
> directory, does the calculation otherwise work?
>
> Then I moved all the files of dssp directory to /usr/local/bin/ and then
>> tried to run do_dssp I am in the same situation.
>>
>
> If the executable in your home directory structure works, but in
> /usr/local/bin it fails, then it could be some sort of permission error.  It
> ultimately doesn't matter where your executable is, /usr/local/bin is
> default, but you can set any other location you like with the DSSP
> environment variable.
>
> -Justin
>
> waiting for your help
>> shahid nayeem
>>
>>  On 5/18/10, *Justin A. Lemkul* mailto:jalem...@vt.edu>>
>> wrote:
>>
>>
>>
>>shahid nayeem wrote:
>>
>>Dear All
>>I downloaded dsspcmbi.tar.gz, and compiled  using command
>>./DsspCompileGCC as given in Readme.txt file. when I try to run
>>do_dssp command in gromacs I get error
>>
>>
>>Well, what happened?
>>
>>
>>Fatal error:
>>DSSP executable (/usr/local/bin/dssp) does not exist (use setenv
>>DSSP)
>>
>>I checked for DSSP executible in /usr/local/bin/ and I couldnt
>>find. I
>>
>>
>>It won't be there unless you put it there and you have re-named it.
>> I believe the default name of the dssp program is "dsspcmbi," which
>>you need to change when you move the executable.
>>
>>http://www.gromacs.org/Documentation/Gromacs_Utilities/do_dssp
>>
>>-Justin
>>
>>even tried dsspcmbi.zip file but again I got the same error. I
>>compiled dssp as root. Now what shoul I do in order to run do_dssp
>>comand of gromacs.
>>Shahid nayeem
>>
>>
>>-- 
>>
>>Justin A. Lemkul
>>Ph.D. Candidate
>>ICTAS Doctoral Scholar
>>MILES-IGERT Trainee
>>Department of Biochemistry
>>Virginia Tech
>>Blacksburg, VA
>>jalemkul[at]vt.edu <http://vt.edu/> | (540) 231-9080
>>http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>
>>
>>-- gmx-users mailing listgmx-users@gromacs.org
>><mailto:gmx-users@gromacs.org>
>>http://lists.gromacs.org/mailman/listinfo/gmx-users
>>Please search the archive at http://www.gromacs.org/search before
>>posting!
>>Please don't post (un)subscribe requests to the list. Use the www
>>interface or send it to gmx-users-requ...@gromacs.org
>><mailto:gmx-users-requ...@gromacs.org>.
>>Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>>
>>
>>
> --
> 
>
> 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 listgmx-users@gromacs.org
> http://lists.g

Re: [gmx-users] DSSP

[shahid nayeem]

Hi
After posting this mail I did some google search and after changing the
executible name to dssp I moved it in /usr/local/bin/ After this when I did
do_dssp it starts running asks to select a group I choose main chain 5, then
it generates some intermediate file and gives error as segmentation fault. I
though this problem was because of the executible in /usr/local/bin/ and
rest of file in another directory say /home/shahid/software/dssp/. For this
first I set the path in ~/.bascrc as
DSSP=/home/shahid/software/dssp/DsspCmbi. I tried to run do_dssp I got the
same intermediate file generated backing up the previous one. Then I moved
all the files of dssp directory to /usr/local/bin/ and then tried to run
do_dssp I am in the same situation.
waiting for your help
shahid nayeem


On 5/18/10, Justin A. Lemkul  wrote:
>
>
>
> shahid nayeem wrote:
>
>> Dear All
>> I downloaded dsspcmbi.tar.gz, and compiled  using command
>> ./DsspCompileGCC as given in Readme.txt file. when I try to run
>> do_dssp command in gromacs I get error
>>
>
> Well, what happened?
>
>
>> Fatal error:
>> DSSP executable (/usr/local/bin/dssp) does not exist (use setenv DSSP)
>>
>> I checked for DSSP executible in /usr/local/bin/ and I couldnt find. I
>>
>
> It won't be there unless you put it there and you have re-named it.  I
> believe the default name of the dssp program is "dsspcmbi," which you need
> to change when you move the executable.
>
> http://www.gromacs.org/Documentation/Gromacs_Utilities/do_dssp
>
> -Justin
>
> even tried dsspcmbi.zip file but again I got the same error. I
>> compiled dssp as root. Now what shoul I do in order to run do_dssp
>> comand of gromacs.
>> Shahid nayeem
>>
>
> --
> 
>
> 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 listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
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>
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[gmx-users] DSSP

[shahid nayeem]

Dear All
I downloaded dsspcmbi.tar.gz, and compiled  using command
./DsspCompileGCC as given in Readme.txt file. when I try to run
do_dssp command in gromacs I get error

Fatal error:
DSSP executable (/usr/local/bin/dssp) does not exist (use setenv DSSP)

I checked for DSSP executible in /usr/local/bin/ and I couldnt find. I
even tried dsspcmbi.zip file but again I got the same error. I
compiled dssp as root. Now what shoul I do in order to run do_dssp
comand of gromacs.
Shahid nayeem
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[gmx-users] xmgrace

[shahid nayeem]

Dear all
I downloaded xmgr-4.1.2.tar.gz and tried to install by following commands.
tar -xvzf xmgr-4.1.2.tar.gz
cd xmgr-4.1.2
./configure
make
make install
But it gives error command xmgr not found.
Please help.
shahid Nayeem
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Re: [gmx-users] protein Aggregation using Gromacs

[shahid nayeem]

Hi
 I have used TANGO Aggrescan, Zyggregator and other online tools but I am
unable to find and pinpoint residue responsible for aggregation. Then I did
MD simulation of the proteins with gromacs at different temperature. Now in
this background I need  suggestion to analyse my MD trajectory.
shahid Nayeem


On 5/12/10, Ran Friedman  wrote:
>
> Hi,
>
> There's no recipie to locate aggregation hot spots based on MD
> simulations. There are many papers on simulations of protein and peptide
> aggregation from which you can draw some ideas, but bear in mind that
> aggregation of more than very few and very small peptides is typically
> much slower than what one can simulate using atomistic MD.
>
> For a quick approach you can use sequence analysis tools, e.g., TANGO
> http://tango.crg.es/
>
> Good luck,
> Ran
>
> --
> --
> Ran Friedman
> Postdoctoral Fellow
> Computational Structural Biology Group (A. Caflisch)
> Department of Biochemistry
> University of Zurich
> Winterthurerstrasse 190
> CH-8057 Zurich, Switzerland
> Tel. +41-44-639
> Email: r.fried...@bioc.uzh.ch
> Skype: ran.friedman
> --
>
> shahid nayeem wrote:
> > Dear all
> > What are the analysis tools which should be used on MD trajectory file
> > in order to find potential aggregation sites of a protein. Anyone can
> > tell me about specific resource material on use of Gromacs to predict
> > protein aggregation hot spots from MD trajectory anlysis.
> > Shahid Nayeem
>
> --
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[gmx-users] protein Aggregation using Gromacs

[shahid nayeem]

Dear all
What are the analysis tools which should be used on MD trajectory file in
order to find potential aggregation sites of a protein. Anyone can tell me
about specific resource material on use of Gromacs to predict protein
aggregation hot spots from MD trajectory anlysis.
Shahid Nayeem
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[gmx-users] confusion about trjconv

[shahid nayeem]

Dear all
when I do long mdrun and the run crashes, I generate new .tpr file to
restart the run. Sometime in order to complete run two or three such
.tpr file is generated after reading previous .trr and .ene files.
After completion of the run when I use trjconv (after combining .trr
files with trjcat) which .tpr file should be used with -s flag the
first .tpr file which is generated with grompp at the start of mdrun
or the last .tpr file generated by tpbconv reading previous .trr and
.ene file. I know that in recent version of gromacs restart can be
done using mdrun supplying .cpt file with -cpi flag. I require answer
of my question regardless of the use of .cpt file.
shahid nayeem
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Re: [gmx-users] more than one peptide in one simulation box

[shahid nayeem]

Hi Mark
How one should be certain that this much  trajectory is long enough to get
coverged ensemble.
Shahid



On 4/27/10, Mark Abraham  wrote:
>
> On 27/04/2010 8:58 PM, Justin A. Lemkul wrote:
>
>>
>>
>> shahid nayeem wrote:
>>
>>> Dear Mark
>>> Following your advice I started using three peptide in one simulation
>>> box. Iwas able to add these with genconf as previously in ordered
>>> manner, generated .gro with genconf, solvated it and after energy
>>> minimization I did MD run for 10ns. Everything ran well. In the end
>>> when I see the trajectory I find unfolding of the original chain but
>>> the two additional peptide introduced through genconf show appearance
>>> of new secondary structures. Even in these two the secondary structure
>>> do not develop at the same point. Why the three equivalent peptide
>>> behave differently in similar environment. How can I explain this
>>> observation. why the first peptide does not show any new secondary
>>> structure. Sholud I go with higher number of molecule. Will it make
>>> any difference if peptides are added in disordered manner and then
>>> simulated.
>>>
>>
>> Initial orientation should likely have nothing to do with it. Perhaps
>> this is even the proper behavior for whatever your peptide is. Is its
>> structure dynamic? Is the size of your peptides large enough to even
>> believe that they would be intrinsically stable? Many model peptides, in
>> isolation, have very transient structures.
>>
>> It could also be that your simulation parameters are poorly chosen, so
>> the force field is breaking down. If you want comments on your .mdp
>> file, please post it.
>>
>
> Indeed. MD is chaotic, and there's no reason to expect all peptides of any
> length to show the same actual behaviour in a trajectory. They might show
> the same behaviour in the limit of a converged ensemble, but only if
> aggregation is not a factor.
>
> Mark
>
>
>  On 4/23/10, *Mark Abraham* >> <mailto:mark.abra...@anu.edu.au>> wrote:
>>>
>>> On 23/04/10 13:16, shahid nayeem wrote:
>>>
>>> Dear All
>>> I am trying to study inter peptide interaction fpr which I need
>>> to put
>>> more than one peptide in one simulation box. I did it with genconf
>>> command but this inserts peptide in a regular ordered manner I want
>>> these to be in irregular disordered insertion. Even after using
>>> genconf
>>>
>>>
>>> Well that's a difficult and atypical scenario. genconf -shuffle will
>>> allow you to stack the same peptide in a regular array with random
>>> rotations of the whole box. Then you can solvate, equilibrate and
>>> run MD at a high temperature to give yourself a quasi-disordered
>>> starting state.
>>>
>>> , I tried to proceed furthe after solvation with spc water. The
>>> energy
>>> minimization (steepest descent) failed to converge even after
>>> 5000 steps
>>> and theirafter position restraint dynamics failed giving
>>> segmentation
>>> fault. Introducing more peptide after generating .gro with -ci -nmol
>>> gives error showing more than one residue in insert molecule.
>>> Please help me and write commands which I should follow.
>>>
>>>
>>> No, because that's an impossible task. We can't begin to guess the
>>> reasons for things failing without seeing the actual output (was the
>>> EM energy large and negative? what was the actual error message
>>> from -ci -nmol?).
>>>
>>> You should be careful to start with a small test case so that you
>>> can learn the workflow with a manageable problem. Can you get a
>>> single peptide to equilibrate? Two stacked peptides? It is best to
>>> learn to walk before trying to run :-)
>>>
>>> Mark
>>> -- gmx-users mailing list gmx-users@gromacs.org
>>> <mailto:gmx-users@gromacs.org>
>>> http://lists.gromacs.org/mailman/listinfo/gmx-users
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>>>
>>>
>>>
>> --
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Re: [gmx-users] more than one peptide in one simulation box

[shahid nayeem]

Hi Justin
Should I try to do position restraint at 500k and then full MD simulation.
shahid


On 4/27/10, Justin A. Lemkul  wrote:
>
>
>
> shahid nayeem wrote:
>
>> My peptide is 26 residue alpha helix obtained from crystal structure  .pdb
>> file. I am posting energy minimization, position restarint and full MD
>> simulation .mdp file
>>
>>
>
> 
>
>
>> ref_t = 300 300
>>
>
> Here, you're equilibrating at 300 K...
>
> 
>
> ref_t = 500 500
>>
>
> and here, you're running MD at 500 K, without any equilibration in between.
> That could be a problem, but more likely, the high temperature is simply
> causing the structure to break down.  Short helices are usually not stable
> in isolation, and heating them to extreme conditions will probably
> accelerate this process. The various results you're seeing with different
> helices may just reflect that you haven't simulated long enough to see
> convergence in the structural features, but from what you've described, I
> expect what you're seeing is entirely normal, and almost predictable.
>
> -Justin
>
>
> --
> 
>
> 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
>
> 
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Re: [gmx-users] more than one peptide in one simulation box

[shahid nayeem]

My peptide is 26 residue alpha helix obtained from crystal structure  .pdb
file. I am posting energy minimization, position restarint and full MD
simulation .mdp file

Energy minimization

cpp = /usr/bin/cpp

define = -DFLEX_SPC

constraints = none

integrator = steep

nsteps = 3000

;

; Energy minimizing stuff

;

emtol = 1000

emstep = 0.01

nstcomm = 1

ns_type = grid

rlist = 0.9

coulombtype = PME

rcoulomb = 0.9

rvdw = 0.9

fourierspacing = 0.14

fourier_nx = 0

fourier_ny = 0

fourier_nz = 0

pme_order = 4

ewald_rtol = 1e-5

optimize_fft = yes

Tcoupl = no

Pcoupl = no

gen_vel = no
Position_restraint.mdp


cpp = /usr/bin/cpp

define = -DPOSRES

constraints = all-bonds

constraintalgorithm = LINCS

integrator = md

dt = 0.002 ; ps !

nsteps = 25000 ; total 50 ps.

nstcomm = 1

nstxout = 500

nstvout = 1000

nstfout = 0

nstlog = 10

nstenergy = 10

nstlist = 10

ns_type = grid

rlist = 0.9

coulombtype = PME

rcoulomb = 0.9

rvdw = 0.9

fourierspacing = 0.14

fourier_nx = 0

fourier_ny = 0

fourier_nz = 0

pme_order = 4

ewald_rtol = 1e-5

optimize_fft = yes

; Berendsen temperature coupling is on in two groups

Tcoupl = berendsen

tc-grps = Protein Non-protein

tau_t = 0.1 0.1

ref_t = 300 300

; Energy monitoring

energygrps = Protein Non-protein

; Pressure coupling is not on

Pcoupl = no

tau_p = 0.5

compressibility = 4.5e-5

ref_p = 1.0

; Generate velocites is on at 300 K.

gen_vel = yes

gen_temp = 300.0

gen_seed = 173529
Full_MD.mdp

cpp = /usr/bin/cpp

constraints = all-bonds

integrator = md

dt = 0.002 ; ps !

nsteps = 500 ; total 1 ps.

nstcomm = 1

nstxout = 5000

nstvout = 4

nstfout = 0

nstlog = 500

nstenergy = 500

nstlist = 10

ns_type = grid

rlist = 0.9

coulombtype = PME

rcoulomb = 0.9

rvdw = 0.9

fourierspacing = 0.14

fourier_nx = 0

fourier_ny = 0

fourier_nz = 0

pme_order = 4

ewald_rtol = 1e-5

optimize_fft = yes

; Berendsen temperature coupling is on in two groups

Tcoupl = berendsen

tc-grps = Protein Non-protein

tau_t = 0.1 0.1

ref_t = 500 500

; Energy monitoring

energygrps = Protein Non-protein

; Isotropic pressure coupling is now on

Pcoupl = berendsen

Pcoupltype = isotropic

tau_p = 0.5

compressibility = 4.5e-5

ref_p = 1.0

; Generate velocites is off at 500 K.

gen_vel = no

gen_temp = 500.0

gen_seed = 173529

 shahid



On 4/27/10, Justin A. Lemkul  wrote:
>
>
>
> shahid nayeem wrote:
>
>> Dear Mark
>> Following your advice I started using three peptide in one simulation box.
>> Iwas able to add these with genconf as previously in ordered manner,
>> generated .gro with genconf, solvated it and after energy minimization I did
>> MD run for 10ns. Everything ran well. In the end when I see the trajectory I
>> find unfolding of the original chain but the two additional peptide
>> introduced through genconf show appearance of new secondary structures. Even
>> in these two the secondary structure do not develop at the same point. Why
>> the three equivalent peptide behave differently in similar environment. How
>> can I explain this observation. why the first peptide does not show any new
>> secondary structure. Sholud I go with higher number of molecule. Will it
>> make any difference if peptides are added in disordered manner and then
>> simulated.
>>
>
> Initial orientation should likely have nothing to do with it.  Perhaps this
> is even the proper behavior for whatever your peptide is.  Is its structure
> dynamic?  Is the size of your peptides large enough to even believe that
> they would be intrinsically stable?  Many model peptides, in isolation, have
> very transient structures.
>
> It could also be that your simulation parameters are poorly chosen, so the
> force field is breaking down.  If you want comments on your .mdp file,
> please post it.
>
> -Justin
>
> Shahid
>>
>>  On 4/23/10, *Mark Abraham* > mark.abra...@anu.edu.au>> wrote:
>>
>>On 23/04/10 13:16, shahid nayeem wrote:
>>
>>Dear All
>>I am trying to study inter peptide interaction fpr which I need
>>to put
>>more than one peptide in one simulation box. I did it with genconf
>>command but this inserts peptide in a regular ordered manner I want
>>these to be in irregular disordered insertion. Even after using
>>genconf
>>
>>
>>Well that's a difficult and atypical scenario. genconf -shuffle will
>>allow you to stack the same peptide in a regular array with random
>>rotations of the whole box. Then you can solvate, equilibrate and
>>run MD at a high temperature to give yourself a quasi-disordered
>>starting state.
>>
>>, I tried to proceed furthe after solvation with spc water. The
>>energy
>>

Re: [gmx-users] more than one peptide in one simulation box

[shahid nayeem]

Dear Mark
Following your advice I started using three peptide in one simulation box.
Iwas able to add these with genconf as previously in ordered manner,
generated .gro with genconf, solvated it and after energy minimization I did
MD run for 10ns. Everything ran well. In the end when I see the trajectory I
find unfolding of the original chain but the two additional peptide
introduced through genconf show appearance of new secondary structures. Even
in these two the secondary structure do not develop at the same point. Why
the three equivalent peptide behave differently in similar environment. How
can I explain this observation. why the first peptide does not show any new
secondary structure. Sholud I go with higher number of molecule. Will it
make any difference if peptides are added in disordered manner and then
simulated.
Shahid



On 4/23/10, Mark Abraham  wrote:
>
> On 23/04/10 13:16, shahid nayeem wrote:
>
>> Dear All
>> I am trying to study inter peptide interaction fpr which I need to put
>> more than one peptide in one simulation box. I did it with genconf
>> command but this inserts peptide in a regular ordered manner I want
>> these to be in irregular disordered insertion. Even after using genconf
>>
>
> Well that's a difficult and atypical scenario. genconf -shuffle will allow
> you to stack the same peptide in a regular array with random rotations of
> the whole box. Then you can solvate, equilibrate and run MD at a high
> temperature to give yourself a quasi-disordered starting state.
>
> , I tried to proceed furthe after solvation with spc water. The energy
>> minimization (steepest descent) failed to converge even after 5000 steps
>> and theirafter position restraint dynamics failed giving segmentation
>> fault. Introducing more peptide after generating .gro with -ci -nmol
>> gives error showing more than one residue in insert molecule.
>> Please help me and write  commands which I should follow.
>>
>
> No, because that's an impossible task. We can't begin to guess the reasons
> for things failing without seeing the actual output (was the EM energy large
> and negative? what was the actual error message  from -ci -nmol?).
>
> You should be careful to start with a small test case so that you can learn
> the workflow with a manageable problem. Can you get a single peptide to
> equilibrate? Two stacked peptides? It is best to learn to walk before trying
> to run :-)
>
> Mark
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
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[gmx-users] more than one peptide in one simulation box

[shahid nayeem]

Dear All
I am trying to study inter peptide interaction fpr which I need to put more
than one peptide in one simulation box. I did it with genconf command but
this inserts peptide in a regular ordered manner I want these to be in
irregular disordered insertion. Even after using genconf , I tried to
proceed furthe after solvation with spc water. The energy minimization
(steepest descent) failed to converge even after 5000 steps and theirafter
position restraint dynamics failed giving segmentation fault. Introducing
more peptide after generating .gro with -ci -nmol gives error showing more
than one residue in insert molecule.
Please help me and write  commands which I should follow.
Shahid Nayeem
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Re: [gmx-users] genbox

[shahid nayeem]

I was also trying to put more than one protein in one simulation box. I was
able to do it with genconf but it appears that the addition is in very
ordered manner if one looks .gro file in VMD. How can I add these protein in
disordered random orientation.
msnayeem


On 4/20/10, Justin A. Lemkul  wrote:
>
>
>
> fahimeh bafti wrote:
>
>> Thanks :)
>> but I couldn't manage with that, it makes the same error with editconf as
>> well, the problem was related to having more than one residue inside
>> insert.gro
>>
>
> editconf should not have a problem placing multi-residue molecules within a
> box.  That is its main function, so I can only assume you did something
> wrong.
>
> I did it at the end with genconf
>>
>> genconf  -nbox 2 2 2 (as u want)  -f  file.gro  -o file_replicate.pdb
>>
>> it will simply replicate the unit.
>>
>>
> That works.  Glad you found a solution.
>
> -Justin
>
>  Fahimeh
>>
>>  > Date: Tue, 20 Apr 2010 09:12:44 -0400
>>  > From: jalem...@vt.edu
>>  > To: gmx-users@gromacs.org
>>  > Subject: Re: [gmx-users] genbox
>>  >
>>  >
>>  >
>>  > fahimeh bafti wrote:
>>  > > Thank you Justin
>>  > > but I end up with a new error. now in the insert.pdp file I have a
>>  > > molecule which I need to add 4 copy of that inside the solute.pdb
>>  > > genbox_d -ci insert.pdb -nmol 4 -cp solute.pdb
>>  > >
>>  > > but it gave me:
>>  > >
>>  > > Fatal error:
>>  > > more then one residue in insert molecules
>>  > > program terminated
>>  > >
>>  >
>>  > Then you have two options:
>>  >
>>  > 1. Use the development (git) version of the code, which I believe can
>> now deal
>>  > with multi-residue molecules.
>>  > 2. Use editconf to position all the components of your system.
>>  >
>>  > You could, I suppose, hack your "insert.pdb" to contain one residue
>> (i.e.,
>>  > through renaming and renumbering) and then convert it back, but that
>> sounds like
>>  > a mess. Probably #2 is the easiest.
>>  >
>>  > -Justin
>>  >
>>  > > Fahimeh
>>  > >
>>  > >
>>  > > > Date: Tue, 20 Apr 2010 07:10:59 -0400
>>  > > > From: jalem...@vt.edu
>>  > > > To: gmx-users@gromacs.org
>>  > > > Subject: Re: [gmx-users] genbox
>>  > > >
>>  > > >
>>  > > >
>>  > > > fahimeh bafti
>>  > > > > Hello,
>>  > > > >
>>  > > > > I want to use a file.pdb which has 8 chain of polypeptide, each
>> chain
>>  > > > > contains 6 residues. I need to expand it to 12 chains of 6
>> rsidues
>>  > > so I
>>  > > > > need to add 4 chains or in the other word 24 residues. I think I
>>  > > have to
>>  > > > > use genbox, so I make another copy of file.pdb and rename it to
>>  > > > > insert.pdb and i used this command, but it doesn't work.
>>  > > > >
>>  > > > > genbox -cp file.pdb -ci insert.pdb -nmole 24 -o out.gro
>>  > > > >
>>  > > > > can anybody help me?
>>  > > >
>>  > > > The implication with genbox -ci -nmol is that the coordinate file
>>  > > passed to -ci
>>  > > > contains one molecule, and an additional -nmol molecules are
>>  > > inserted. So if
>>  > > > you already have 8, you need a coordinate file with one polypeptide
>>  > > and then:
>>  > > >
>>  > > > genbox -ci insert.pdb -nmol 4
>>  > > >
>>  > > > Note in the documentation that -nmol refers to the number of
>>  > > molecules, not a
>>  > > > number of residues, which I think is the root of your problem.
>>  > > >
>>  > > > -Justin
>>  > > >
>>  > > > >
>>  > > > > Fahimeh
>>  > > > >
>>  > > > >
>>  > >
>> 
>>  > > > > Hotmail: Trusted email with powerful SPAM protection. Sign up
>> now.
>>  > > > > 
>>  > > > >
>>  > > >
>>  > > > --
>>  > > > 
>>  > > >
>>  > > > 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
>>  > > >
>>  > > > 
>>  > > > --
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>>  > --
>>  > 
>>  >
>>  > Justin A. Lemkul
>>  > Ph.D. Candidate
>>  > ICTAS Doctoral Scholar
>>  > MILES-IGERT Trainee
>>  > Department of Biochemistry
>>  > Virginia Tech
>>