>
> On 5/16/18 3:32 AM, Naba wrote:
> > Dear all,
> >
> > I am using gromacs 5.1.2 and trying to pull both monomers of 128 amino
> > acids from its homodimer in opposite directions along z axis. The
> > interfaces of each protein chain is parallel to the z axis. I do not need
> > any restraints in
Dear all,
Do we need to change any other parameters other than ref_t and gen_temp
should be changed if I want to perform protein protein complex md
simulation at different temperatures of the same input protein. Is it
necessary to equilibrate the average pressure value to 1 bar before running
the f
Hi all,
I think I understand how it works, but to double-check... There's a paper
describing a setup of intramolecular interactions for boron nitride (
https://pubs.acs.org/doi/10.1021/acs.jpclett.7b03443), in which non-bonded
interactions *within* 1-4 were set up in the following way: LJ is off,
On 5/16/18 3:32 AM, Naba wrote:
Dear all,
I am using gromacs 5.1.2 and trying to pull both monomers of 128 amino
acids from its homodimer in opposite directions along z axis. The
interfaces of each protein chain is parallel to the z axis. I do not need
any restraints in this case. I have gone
Hi,
Thanks.
On Wed, May 16, 2018 at 3:09 PM, Mark Abraham
wrote:
> Hi,
>
> I would assume not, because it's more useful to be able to let a user
> specify a table for an energy group and for that to contain different atom
> types.
>
I'm afraid I did get your point!
What I know is that the potent
Hi,
I would assume not, because it's more useful to be able to let a user
specify a table for an energy group and for that to contain different atom
types.
But your best friend is to test both your understanding and the code by
e.g. making a structure file with two such atoms 1nm apart and observ
Hi,
Suppose that the C6 and C12 for the nonbonded interaction between two beads
of P4 and SNa in the Martini force fields are as following:
C6 C12
P4SNda1 0.17246E-00 0.18590E-02 ; semi attractive
Now, I was wondering how I ca
Dear all,
I want to create a topol.top file for Silica slab for which the force
fields parameters are available in literature as well as in the lammps.data
file which works fine in lammps (below links). The slab has in general 2184
atom including two types of O atom(OS in surface part and OB in the
You may want to familiarize yourself with how the terminal works before
proceeding. You need to give the path on your machine for dssp.
On Wed, May 16, 2018 at 12:13 PM, SHAHEE ISLAM
wrote:
> when i am using command
> dssp -h
> below are shown on the terminal screen
> DSSP 2.0.4 options:
> -h
when i am using command
dssp -h
below are shown on the terminal screen
DSSP 2.0.4 options:
-h [ --help ] Display help message
-i [ --input ] argInput file
-o [ --output ] arg Output file, use 'stdout' to output to screen
-v [ --verbose ] Verbose output
--version
Hello,
for metal ions (and especially transition metals) you should first
consider what kind of metal model you want to employ, as the different
models (bonded, soft sphere or dummy model) have have different properties.
There are numerous papers outlining the parametrization of those
differen
Have you tried running the dssp command on a pdb file to ensure that it is
working as intended? FYI 4.5.5 is no longer supported so you may want to
consider upgrading to (the much faster) gromacs 2018.
On Wed, May 16, 2018 at 11:45 AM, SHAHEE ISLAM
wrote:
> i have installed dssp2.04 in usr/local
Dear All,
I need to simulation of protein-ligand with coordinated metal ion bound to
ligand. The metal ion is Mn+2, Advise me whether its correct to use
CHARMM36 and OPLSS force field for parameterization? What things should
taken care while simulating such cases where we have metals with unpaired
i have installed dssp2.04 in usr/local/bin.
On 5/16/18, Joe Jordan wrote:
> You have to point to where you have dssp installed. This may require you to
> install dssp.
>
> On Wed, May 16, 2018 at 11:41 AM, SHAHEE ISLAM
> wrote:
>
>> i want calculate the secondary structure of protein in gromacs.
You have to point to where you have dssp installed. This may require you to
install dssp.
On Wed, May 16, 2018 at 11:41 AM, SHAHEE ISLAM
wrote:
> i want calculate the secondary structure of protein in gromacs.but
> when i am using this command
>
> do_dssp -f dynamic.xtc -s dynamic.tpr -sc scount
i want calculate the secondary structure of protein in gromacs.but
when i am using this command
do_dssp -f dynamic.xtc -s dynamic.tpr -sc scount.xvg -o ss.xpm -dt 10
getting this error
Program do_dssp, VERSION 4.5.5
Source code file: /build/buildd/gromacs-4.5.5/src/tools/do_dssp.c, line: 572
Fat
Dear all,
I am using gromacs 5.1.2 and trying to pull both monomers of 128 amino
acids from its homodimer in opposite directions along z axis. The
interfaces of each protein chain is parallel to the z axis. I do not need
any restraints in this case. I have gone through the GROMACS manual and
some
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