On 4/10/2011 5:20 PM, MARY VARUGHESE wrote:
Hi,
I , am working on interaction between proteins/nucleic acids and ligands.
On deriving partial atomic charges using gaussian can anyone suggest,
among HF-6-31G* and B3LYP-6-31G which one is ideal(or any other one to
suggest) and why?
I mean to get
*Dear all,
I have been trying to generate pre-equilibrated ethanol solvent
box of 512 molecules in **OPLSAA ff. I used ethanol.itp in oplsaa.ff
directory for generating the topology file for ethanol. After NVT
equilibration some of the molecules get aggregated and there is some void
Hi all,
Let's say I created a pdb of a B-DNA Double-Helix with amber tools. Now
I would like to have a topology in which the last residues are bonded to
the first. How can I do that expect of actually mess together a topology
file by self written scripts and/or handwork? Also if create helix
any hints? :(
03 Ekim 2011 22:32 tarihinde ahmet yıldırım ahmedo...@gmail.com yazdı:
I look at chapter 8 but I didnt found that I want. can you give a hint?
Thanks
2011/10/3 Mark Abraham mark.abra...@anu.edu.au
On 3/10/2011 10:29 PM, ahmet yıldırım wrote:
Dear users,
How can I
On 4/10/2011 7:05 PM, ahmet y?ld?r?m wrote:
any hints? :(
You didn't find something useful in the section titled Root mean square
deviations in structure?
Mark
03 Ekim 2011 22:32 tarihinde ahmet y?ld?r?m ahmedo...@gmail.com
mailto:ahmedo...@gmail.com yazd?:
I look at chapter 8 but
On 4/10/2011 6:16 PM, Ravi Kumar Venkatraman wrote:
*Dear all,
I have been trying to generate pre-equilibrated ethanol
solvent box of 512 molecules in **OPLSAA ff. I used ethanol.itp in
oplsaa.ff directory for generating the topology file for ethanol.
After NVT equilibration some
On 4/10/2011 6:25 PM, Wojciech Müller wrote:
Hi all,
Let's say I created a pdb of a B-DNA Double-Helix with amber tools.
Now I would like to have a topology in which the last residues are
bonded to the first. How can I do that expect of actually mess
together a topology file by self written
Hi,
I read the standard advice for parametrization.
But,
Can anyone suggest the ideal force field and QM method( for paramterization
using gaussian say, HF, DFT etc) to study the interaction between a protein and
a ligand when i am using GROMCAs simulation program.
Thanking you
Mary
--- On
No, it calculates with respect to the positions atom. but I want to
calculate the RMSD bonds (A˚ ) and RMSD angles (o).
2011/10/4 Mark Abraham mark.abra...@anu.edu.au
On 4/10/2011 7:05 PM, ahmet yıldırım wrote:
any hints? :(
You didn't find something useful in the section titled Root mean
MARY VARUGHESE wrote:
Hi,
I read the standard advice for parametrization.
But,
Can anyone suggest the ideal force field and QM method( for
paramterization using gaussian say, HF, DFT etc) to study the
interaction between a protein and a ligand when i am using GROMCAs
simulation program.
Hi!
I'm performing the analysis of a 30 residues PVA polymer chain in SPC water.
I'm trying to find the dihedral transition times of each residue (possibly
as an histogram 'number of transitions vs. residue number').
I've already tried:
1) g_angle -f traj.trr -s topol.tpr -n angle.ndx -oh
Giulio Tesei wrote:
Hi!
I'm performing the analysis of a 30 residues PVA polymer chain in SPC
water.
I'm trying to find the dihedral transition times of each residue
(possibly as an histogram 'number of transitions vs. residue number').
I've already tried:
1) g_angle -f traj.trr -s
Hi guys,
I was just wondering if with direction_periodic the pull simulations pulls at
both ends of the protein rather than just one.
I've previously been position restraining the C-terminus of my protein and
pulling on the N-terminus. With the distance pull code this seems to do
exactly
I'm sorry, actually I forgot to add the flag in the email but I added it
when I started the program.
g_angle -f traj.trr -s topol.tpr -n dihe.ndx -oh histo.xvg -type dihedral
I get the following output:
Group 0 (Phi=0.0_3_5.92) has 232 elements
There is one group in the index
Reading file
i see the instructions on the web:
Installing
Download and unpack the binary package for the respective OS and
architecture. Copy the content of the package to your normal Gromacs
installation directory (or to a custom location). Note that the
distributed Gromacs-GPU packages do not contain the
On 5/10/2011 2:10 AM, 杜波 wrote:
i see the instructions on the web:
Installing
Download and unpack the binary package for the respective OS and
You are instructed to get a binary package. However, above this text is
an updated set of instructions that declares the binary packages are
Hey :)
If that is what you want, you'll have to turn to programming. But what do
you think to gain from it? First get to the bottom of things you can do with
gromacs already. Then, if the tools available don't help in answering your
question, think of what you'd need to get it done.
Cheers,
I'm using gromacs version 4.0.5. My system is a double stranded DNA (9
nucleotides), a bit modified (the DC3 terminal is replaced by another
one named C5l). When I try to convert the pdb file to a .gro one, a
message error appear, as follows:
/
Fatal error:
There is a dangling bond at at least
Hi Gromac Users,
I stupidly overwritten my .edr file, but my .traj file is still intact. Is it
possible to use my traj file to recover my energy file. I also have my tpr file
which is also in one piece.
Thanks,
Taylor
--
gmx-users mailing listgmx-users@gromacs.org
On 10/04/2011 09:48 PM, Taylor Kaplan wrote:
Hi Gromac Users,
I stupidly overwritten my .edr file, but my .traj file is still intact. Is
it possible to use my traj file to recover my energy file. I also have my tpr
file which is also in one piece.
Thanks,
Taylor
Hi Taylor,
you can
Sounds very much like you have an insufficient number of molecules in the box
to fill it up. If you look at the pressure data for the simulation, I suspect
you will find that it is negative, the box wants to decrease in volume.
Catch ya,
Dr. Dallas Warren
Medicinal Chemistry and Drug Action
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