Hi,
I have a protein of interest which requires distance restraint for C alpha
atoms. However, the simulation does not seem to include the restraint at
all.
*prod.mdp*
define = -DPOSRES
constraints = none
integrator = md
dt = 0.005
nsteps
Dear users,
I would like to perform an umbrella sampling by pulling two metal ions (two
pull groups) away from protein (reference group) in opposite directions. I
could restrain the positions of protein atoms (reference group) and then
perform the pulling simulation. But how do I ensure that one
Dear all
For hydrogen bond analysis, we generate *.xvg file for -num tag in gmx
hbond command. My inquiry is in the xvg file there are three column
output. First column is time. Which one is hydrogen bond number?
If number 2 column is hydrogen bond number in every frame than what is
number 3
Simply copy/paste the text from the coordinate file for the nano
particle onto the end of the coordinate file for the monolayer. Of
course, you need to only insert the coordinate lines, not the text at
the start (description and number of atoms in a .gro file) or end (box
dimensions in a .gro
thank you very much
I tried to complete pdb file, but since pdb file containing phosphoserine
which is different from its sequence, because there is serine in its
sequence file, when I wanted to use modeller, I confronted these error "
sequence difference between alignment and pdb.
I used
Hi Mark,
I decided to write my own script, which computes distances between silica
and protein atoms as you suggested. Removing the silica is not trivial
because one must remove SiO2 molecules but there is no unique way to
partition a silica block into SiO2 molecules.
.Jose
On Fri, Jun 16, 2017
On 6/18/17 2:19 PM, marzieh dehghan wrote:
Hi
Dear Justin
Thanks a lot for your kind answer, I applied two types of command to get
rid of the previous error
*at first*, the following command was used:
*gmx pdb2gmx -f *.pdb -o *.gro -p topol.top -ignh -water spc *
but I confronted these
Hi
Dear Justin
Thanks a lot for your kind answer, I applied two types of command to get
rid of the previous error
*at first*, the following command was used:
*gmx pdb2gmx -f *.pdb -o *.gro -p topol.top -ignh -water spc *
but I confronted these error
CYS901 SG7090 1.414
CYS905 SG7117
> On 18. Jun 2017, at 13:40, Vries, de, H.W.
> wrote:
>
> dear all,
>
> I am employing the computational electrophysiology scheme in gromacs 5.1.4.
> I want to set a bulk-offset parameter, such that the scheme only does
> position exchanges in a region that is
dear all,
I am employing the computational electrophysiology scheme in gromacs 5.1.4.
I want to set a bulk-offset parameter, such that the scheme only does
position exchanges in a region that is remotely enough from my protein.
However, it seems that I am not able to set the 'bulk-offset'
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