Dear Tsjerk,
Thanks for your reply. I am
interested to work with ganglioside GM1. In that case which ffG will be
appropriate for me.
Ms. Anindita Gayen
C/O Dr. Chaitali Mukhopadhyay
Senior Research Fellow
Department of Chemistry
University of Calcutta
92, A. P. C. Road
Hi Anindita,
I was sort of afraid you might be dealing with glycosphingolipids. The
Gromos force fields do not have properly behaving models for
sphingolipids yet. I'm not sure whether other force fields do much
better. There's some serious parameterization to do here. If you have
experimenal
Hello Payman,
Westgrid (and Glacier) has several pages of doc on its website about
running Gromacs and compiling softwares. I used to run (my own
compilation of) Gromacs on Glacier and never had any particular problem.
You just have to make sure you compile it with the correct mpicc and
fftw
Hi Nehme,
I've did simulations on TRAIL, which also contains a zinc-finger
domain, involving three cysteines and a chloride ion. But it's not so
simple. Luckily the exact parameters seemed not that vital, as the
zinc apparently functions to keep the three subunits together and was
in any case not
Hi,
On Tue, 19 May 2009 14:23:07 -0600, Payman Pirzadeh wrote
Hi Justin,
Following is the script I use. But remember several points:
${MPIRUN} -np $NUM_PROCS -machinefile $PBS_NODEFILE -path
./global/home/pirzadeh/gromacs-4.0.4/bin/mdrun_d -deffnm npttest
You have a dot before /global/...
I tried to install Gromacs on my Core2Quad pc with the command
./configure --enable-mpi --disable-nice --program-suffix=_mpi
it is showing the following error result:
[sand...@bhanu gromacs-4.0.3]$ ./configure --enable-mpi --disable-nice --program
-suffix=_mpi
checking build system type...
Bhanu wrote:
I tried to install Gromacs on my Core2Quad pc with the command
./configure --enable-mpi --disable-nice --program-suffix=_mpi
it is showing the following error result:
[sand...@bhanu gromacs-4.0.3]$ ./configure --enable-mpi --disable-nice --program
-suffix=_mpi
checking build
Thanks Justin, will try your suggestion..
2009/5/20 Justin A. Lemkul jalem...@vt.edu:
Bhanu wrote:
I tried to install Gromacs on my Core2Quad pc with the command
./configure --enable-mpi --disable-nice --program-suffix=_mpi
it is showing the following error result:
[sand...@bhanu
Hi all,
I have some doubts regarding the general use of acfs.
The molecule I am studying is formed by two polycyclic aromatic
sub-units joined by a 20-alkene chain; it is something like this:
/--\/--\ /--\/--\
A | | |-CH2-CH-CH2-CH-CH2(...)| | | B
\--/\--/
Dear all,
i have a simple question regarding definition of proper improper
dihedral type in gromacs. As in ffgmxbon.itp.
[ dihedraltypes ]
; j k func phi0 cp mult
C OA 1 180.000 16.736
Hello
I had a problem with mdrun while trying to run trajectories for protein
ligand complexes. I`ve already done successful calculations with 60
complexes, unfortunately 4 complexes gave the following error. The entire
output is too big to copy, so I have only copied the error part. But lots of
Jocley Araujo wrote:
Hello
I had a problem with mdrun while trying to run trajectories for protein
ligand complexes. I`ve already done successful calculations with 60
complexes, unfortunately 4 complexes gave the following error. The
entire output is too big to copy, so I have only copied the
Jocley Araujo wrote:
Hello
I had a problem with mdrun while trying to run trajectories for protein
ligand complexes. I`ve already done successful calculations with 60
complexes, unfortunately 4 complexes gave the following error. The
entire output is too big to copy, so I have only copied
Hi Justin
I am trying to prep a pdb file for md but keep on getting this error message
Fatal error:
Chain identifier 'O' was used in two non-sequential blocks (residue 2400, atom
18726)
Fatal error:
But when I look at the file I only have one chain identifier.
Also when I strip off hydrogens
It would be very advantageous for me to have a g_clustsize that
could implement the Jarvis-Patrick method instead of single linkage.
Would this be very difficult to achieve? Or would it be easy enough to
use source code from g_cluster and do a sort of transplant? Thank
you for you help
David
ANINDITA GAYEN wrote:
Dear all,
i have a simple question regarding definition of proper
improper dihedral type in gromacs. As in ffgmxbon.itp
please upgrade your force field. For most force fields there is a proper
description but there is not for this one. Therefore we
Please keep all Gromacs-related correspondence on the gmx-users list; I do not
advertise as a free tutor :)
yimnai forlemu wrote:
Hi Justin
I am trying to prep a pdb file for md but keep on getting this error message
Fatal error:
Chain identifier 'O' was used in two non-sequential blocks
Jacob Spooner wrote:
It would be very advantageous for me to have a g_clustsize that
could implement the Jarvis-Patrick method instead of single linkage.
Would this be very difficult to achieve? Or would it be easy enough to
use source code from g_cluster and do a sort of transplant? Thank
you
Hi ALL,
I am simulating a GPCR protein in a POPC bilayer.
I have followed Justins' tutorial to set up the system, but have used POPC
instead of DPPC. I have used the same parameters given in that tutorial. Till
equilibration everything went well. But after releasing the protein in the
What exactly do you mean by unusual cross bonds?
I suspect what you are seeing is simply a visualisation artifact, with a
molecule being displayed across a PBC in the viewer you are using.
Catch ya,
Dr. Dallas Warren
Department of Pharmaceutical Biology and Pharmacology
Pharmacy and
Anirban Ghosh wrote:
Hi ALL,
I am simulating a GPCR protein in a POPC bilayer.
I have followed Justins' tutorial to set up the system, but have used
POPC instead of DPPC. I have used the same parameters given in that
tutorial. Till equilibration everything went well. But after releasing
the
the lipids are forming usual cross bonds (seen in the form of long
straight lines)
lines? on what? You need to do a much better job of describing your
problem and your observations before anyone can give you a better
suggestion than remove those lines and everything will be solved...
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