Dear Mark,
I think that i couldn't explain my problem clearly, however i have changed
my .rtp but i don't know how should be my .hdb file.
a) The structure of *BOC* is: *-CO-CH2-CH(C6H5Cl)-CH2-NH-*
b) This is the new charges:
[ BOC ]
[ atoms ]
Nopls_238 -0.500 1
H
On 14/11/2010 7:26 PM, hengame fallah wrote:
Dear Mark,
I think that i couldn't explain my problem clearly, however i have
changed my .rtp but i don't know how should be my .hdb file.
a) The structure of *_BOC_* is: *-CO-CH2-CH(C6H5Cl)-CH2-NH-*
Great.
b) This is the new charges:
[ BOC ]
Dear Mark
I have a question as same as atila petrosian, but my system is protein-dna.
you said [IIRC g_select has some better documentation available once you run
it and ask for help, somewhat like make_ndx].
please explain IIRC more. Is IIRC a program or a list of archives?
any help will
On 14/11/2010 7:57 PM, leila karami wrote:
Dear Mark
I have a question as same as atila petrosian, but my system is
protein-dna.
you said [IIRC g_select has some better documentation available once
you run it and ask for help, somewhat like make_ndx].
please explain IIRC more. Is IIRC a
I read about .hdb file and then i editted my .hdb file:
...
BOC 9
11H N -CCA
26HA CA N CB
15HB CB CA CG1CG2
11HD1CD1CG1CE1
11HD2CD2CG1CE2
11HE1CE1CD1CZ
1
On 14/11/2010 8:13 PM, hengame fallah wrote:
I read about .hdb file and then i editted my .hdb file:
...
BOC 9
Then you'll know from your reading what this number should be :-) It's
the number of types of hydrogen atoms that might be added. For each of
them, there's one line below. You
Amin Arabbagheri wrote:
Dear All,
I'm simulating a DNA duplex using amber99p. starting the simulation(step
0) i face an error which tells:
starting mdrun 'Protein in water'
50 steps,500.0 ps.
step 0Warning: 1-4 interaction between 136 and 179 at distance
96871502.536 which is
Dear gromacs users
I was trying to count waters involved in the interface between Protein_A and
Protein_B.
I made a selection.dat file as follows:
waterO = group SOL and name OW;
heavy1 = group Protein_A and group Protein-H;
heavy2 = group Protein_B and group Protein-H;
inter = waterO and
Dear All,
I would like to get little feedback of my findings/experience with recent
simulations I did with the CHARMM force field in GROMACS and the
-chargegroup options with pdb2gmx. I have performed two simulations with a
helical peptide (25 AA) in a cubic box filled with explicit TIP3P water.
Hi Mark,
Thanks (again, again) for your input!
On Fri, Nov 12, 2010 at 5:35 PM, Mark Abraham mark.abra...@anu.edu.auwrote:
On 13/11/2010 12:49 AM, Martin Kamp Jensen wrote:
Hi,
As far as I understand, a topology (a .top file) and a conformation
(e.g., a .gro file) contain enough
We have a visualization tool that allows us to visualize the changes
in the energy during energy minimization.
The areas with more intense color are those where the atoms contribute
the most to the total energy value.
I just wrote a plug-in to use Gromacs for energy minimizations (or MD
On 15/11/2010 4:13 AM, Martin Kamp Jensen wrote:
Hi Mark,
Thanks (again, again) for your input!
On Fri, Nov 12, 2010 at 5:35 PM, Mark Abraham mark.abra...@anu.edu.au
mailto:mark.abra...@anu.edu.au wrote:
On 13/11/2010 12:49 AM, Martin Kamp Jensen wrote:
Hi,
As far as I
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