Dear all
Please suggest me a tool with which I can generate insertion mutants
from a .pdb file. I want to insert new 10-15 aa sequence of AA in
between an existing .pdb file. The tool should write a new .pdb file
with altered coordinates after insertion of new sequence and
minimization of the stru
Thanks a lot Justin.
On Wed, Aug 29, 2012 at 11:57 PM, Justin Lemkul wrote:
>
>
> On 8/29/12 2:19 PM, tarak karmakar wrote:
>>
>> Dear All,
>>
>> In my protein pdb file I am changing the protonation state of residue
>> and giving some other name to it . Now after creating the .gro file I
>>
Hi,
the OpenMM code is still under review. You can download it using
git fetch https://gerrit.gromacs.org/gromacs refs/changes/83/1283/14 && git
checkout FETCH_HEAD
You can check https://gerrit.gromacs.org/#/c/1283/ for the latest version
of it (as of time of writing the above line gives you the l
Dear All,
In order to calculate the binding free energy of a ligand to a protein
I am using Thermodynamic Integration, i.e. making the ligand "disappear".
Because this ligand is charged (-1), at lambdas different than zero
(when the ligand is already fading) the total system charge incr
Thanks Francesca but even after commenting out the coupling parameters in the
mdp file if I run mdrun without the '-coarse' option I still get the error
that the xtc file cannot be written.
However like I mentioned I am running my simulations with a newer version of
Gromacs after releasing the re
On 8/29/12 2:19 PM, tarak karmakar wrote:
Dear All,
In my protein pdb file I am changing the protonation state of residue
and giving some other name to it . Now after creating the .gro file I
see that the residue present before the modified one has been
considered as the C-terminal and it is
Dear All,
In my protein pdb file I am changing the protonation state of residue
and giving some other name to it . Now after creating the .gro file I
see that the residue present before the modified one has been
considered as the C-terminal and it is adding one extra oxygen atom to
it. I am givin
On 30/08/2012 3:18 AM, Delmotte, Antoine wrote:
Many thanks for your quick response, Mark.
So epsilon_r is actually different from the actual relative
permittivity (which would be like 80 for water), is that right?
You can have an atomistic solvent or a continuum solvent, but not both
at onc
On 30/08/2012 3:43 AM, jesmin jahan wrote:
Hi Justin,
Thanks a lot for your reply. I really appreciate the gromacs_user
folrun help line.
I see! thats why you are not receiving any attachment!
My goal is to compute only GB-energy. I have computed only GB- energy
using Amber and Other packages.
Hi Justin,
Thanks a lot for your reply. I really appreciate the gromacs_user
folrun help line.
I see! thats why you are not receiving any attachment!
My goal is to compute only GB-energy. I have computed only GB- energy
using Amber and Other packages. Now I am using Gromacs to do the same.
As su
Many thanks for your quick response, Mark.
So epsilon_r is actually different from the actual relative permittivity
(which would be like 80 for water), is that right?
If so, how does one usually chooses this value of epsilon_r? Is the
default value of 1 applicable for most cases (like for sim
On 8/29/12 1:06 PM, jesmin jahan wrote:
Dear Justin,
Thanks for your reply.
Here is the CMV.log file . Please check it.
What you've posted is output from grompp. Note that if you're trying to send
attachments, the list rejects them.
Actually, the .pdb file I am using is already minimi
Dear Justin,
Thanks for your reply.
Here is the CMV.log file . Please check it.
Actually, the .pdb file I am using is already minimized and we are
using the same file for amber 11 and Octree based molecular dynamic
package.
I will also do the minimization step to see what happens.
One thing I a
On 8/29/12 12:33 PM, Krzysztof Murzyn wrote:
Justin, Thank you very much. I assume that pairs in pairtypes are used to
calculate 1-4 VdW interactions only and do not influence calculations of
short range VdW?
Correct. You can do a quick single-point energy calculation with the original
and
Justin, Thank you very much. I assume that pairs in pairtypes are used to
calculate 1-4 VdW interactions only and do not influence calculations of
short range VdW?
Regards,
km.
On Wed, Aug 29, 2012 at 6:10 PM, Justin Lemkul wrote:
>
>
> On 8/29/12 11:37 AM, Krzysztof Murzyn wrote:
>
>> Hi,
>>
>
On 8/29/12 11:37 AM, Krzysztof Murzyn wrote:
Hi,
I want to influence slightly the way VdW interactions are calculated by
providing customized values of sigma/epsilon in [ pairtypes ]. I employ
OPLS/AA. The section of my molecule definition looks like, say:
[ pairtypes ]
CT CT 1 0.33 0.2
Whe
On 8/29/12 11:27 AM, jesmin jahan wrote:
Ops!
Thanks Justin for you quick reply.
Sorry, I have attached a log file from previous run. I am attaching
the correct log file here. Please have a look.
I don't see a new .log file attached anywhere.
Actually, I am a Computer Science student. I d
On 08/30/2012 01:11 AM, jesmin jahan wrote:
Thanks Mark for your reply.
For the time being, I admit your claim that I am comparing apple with orange.
So, to investigate more, I run the simulation without any modification
in parameter fields and force field I am using. My test data is CMV
virus s
Hi,
I want to influence slightly the way VdW interactions are calculated by
providing customized values of sigma/epsilon in [ pairtypes ]. I employ
OPLS/AA. The section of my molecule definition looks like, say:
[ pairtypes ]
CT CT 1 0.33 0.2
When I run grompp I get the following error message:
Ops!
Thanks Justin for you quick reply.
Sorry, I have attached a log file from previous run. I am attaching
the correct log file here. Please have a look.
Actually, I am a Computer Science student. I do not have enough
background of Molecular Dynamics.
I am using these three commands and
pdb2gmx
On 8/29/12 11:11 AM, jesmin jahan wrote:
Thanks Mark for your reply.
For the time being, I admit your claim that I am comparing apple with orange.
So, to investigate more, I run the simulation without any modification
in parameter fields and force field I am using. My test data is CMV
virus sh
Thanks Mark for your reply.
For the time being, I admit your claim that I am comparing apple with orange.
So, to investigate more, I run the simulation without any modification
in parameter fields and force field I am using. My test data is CMV
virus shell.
I am using the following commands.
pdb2
Thanks David and Szilárd.
I am attaching a log file that I have got from my experiment. Please
have a look. It says, gromacs version 4.6-dev
I am using :-) VERSION 4.6-dev-20120820-87e5bcf (-: of Gromacs.
I have used the commands:
git clone git://git.gromacs.org/gromacs.git
cd gromacs
git che
On 08/29/2012 11:08 PM, Delmotte, Antoine wrote:
Dear Gromacs users,
I would like to know which charges are used by Gromacs in the
calculation of electrostatic interactions in the standard coulomb
potential:
E_electrostatics = 138.935 * q1 * q2 / (epsilon_r * r_12);
Are q1 and q2 the value
On 08/29/2012 09:33 PM, Bala subramanian wrote:
Hi Mark,
Thanks. I tried defining the rdist in several ways and each time i get
an error as follows, and the last definition of rdist is infact very
similar to what is shown in examples.Could you suggest what is the
mistake i'm doing here.
You're
Dear Gromacs users,
I would like to know which charges are used by Gromacs in the
calculation of electrostatic interactions in the standard coulomb potential:
E_electrostatics = 138.935 * q1 * q2 / (epsilon_r * r_12);
Are q1 and q2 the values tabulated in the file "aminoacids.rtp" of the
fo
Thanx for your nice comment
On Aug 29, 2012 12:54 AM, "Szilárd Páll" wrote:
> On Fri, Aug 17, 2012 at 7:19 PM, Hossein Lanjanian
> wrote:
> > Hi
> >
> > we are new academic users of GROMACS. we installed gromacs 4.5.5 and
> > tried to learn the job by using tutorials found in the "gromacs.org"
>
Hi Mark,
Thanks. I tried defining the rdist in several ways and each time i get
an error as follows, and the last definition of rdist is infact very
similar to what is shown in examples.Could you suggest what is the
mistake i'm doing here.
selection parser: invalid expression value for parameter '
On 29/08/2012 7:43 PM, Bala subramanian wrote:
Hi,
I read the examples. I find that one example shows the usage of rdist
keyword. But i am not getting the right syntax to use it. I tried
several ways as follows to find water within .25-5 nm. Could someone
help me here.
-select 'resname SOL and w
Hi,
I read the examples. I find that one example shows the usage of rdist
keyword. But i am not getting the right syntax to use it. I tried
several ways as follows to find water within .25-5 nm. Could someone
help me here.
-select 'resname SOL and within (0.25 and 0.5) of group "Protein"'
-select
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On Wed, Aug 29, 2012 at 5:32 AM, jesmin jahan wrote:
> Dear All,
>
> I have installed gromacs VERSION 4.6-dev-20120820-87e5bcf with
> -DGMX_MPI=ON . I am assuming as OPENMP is default, it will be
> automatically installed.
>
> My Compiler is
> /opt/apps/intel11_1/mvapich2/1.6/bin/mpicc Intel icc (
On 29/08/2012 4:22 PM, Albert wrote:
Dear:
I am trying to extract one frame of my simulation results by commands:
trjconv -f md.trr -s tuned.tpr -o md.xtc -pbc mol -timestep 100 -n
out.ndx
trjconv -f md.xtc -s tuned.tpr -fit rot+trans -o out.pdb -dump
133000.000 -n out.ndx
However, it said
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