Hi,
I wanted to simulate a beta-hairpin but with the dihedral angle of the turn
residues constrained as per my wish for eg phi angle should not 60 and psi
should be 90. Can anybody tell me how can I do this ??
Regards
--
Bharat
--
gmx-users mailing listgmx-users@gromacs.org
is for the
whole system or for the protein alone. If it's for the system then how can
I get the energy for the protein alone.
On Thu, Jun 14, 2012 at 10:48 AM, Justin A. Lemkul jalem...@vt.edu wrote:
On 6/13/12 9:44 PM, bharat gupta wrote:
Hi,
I wanted to simulate a beta-hairpin
a particular
phi psi angle range
On Thu, Jun 14, 2012 at 11:21 AM, Mark Abraham mark.abra...@anu.edu.auwrote:
On 14/06/2012 12:04 PM, bharat gupta wrote:
Thanks for the reply . Is it possible to calculate the dihedral energy of
certain residues, like in my case for turn residues ??.. How can
which means constraining them simultaneously I want to freeze the other
region of the protein. )
On Thu, Jun 14, 2012 at 3:50 PM, Mark Abraham mark.abra...@anu.edu.auwrote:
On 14/06/2012 4:38 PM, bharat gupta wrote:
Thanks Sir for the reply... This question is related to my first query
would be useful ??
On Thu, Jun 14, 2012 at 4:16 PM, Mark Abraham mark.abra...@anu.edu.auwrote:
On 14/06/2012 4:57 PM, bharat gupta wrote:
I am not going to compare this with anything , I have to look for
sequences and their corresponding energies and select the lowest scoring
ones.
You can't
to be followed during minimization alone. From the previous
answers to my queries I understood how to constrain dihedral space, but I
don't know how to fix the movement of strand residues ?? ... any help will
be highly appreciated.
On Thu, Jun 14, 2012 at 4:24 PM, bharat gupta bharat.85.m
Hi,
I tried restraining two residues of my peptide . The restraints were added
after dihedrals in the top file. Here's how the .top file looks :
[ dihedrals ]
; aiajakal functc0c1
c2c3
16 41817 2
18162019 2
Hi,
I tried restraining two residues of my peptide . The restraints were added
after dihedrals in the top file. Here's how the .top file looks :
[ dihedrals ]
; aiajakal functc0c1
c2c3
16 41817 2
18162019 2
Hi,
I have been trying to study folding of a peptide 24 residues long. I
did a simulation of 50 ns with explicit solvent, CHARMM FF, but I
was not able to find even a single folding event. Then I decided use
explicit solvent for simulation and I again simulated the peptide for
100 ns . This
Hi,
There's a plugin in VMD called volmap which I think can be used for this
kind of analysis.
Bharat
On Sat, Sep 29, 2012 at 9:27 PM, rama david ramadavidgr...@gmail.comwrote:
Hi Gromacs Users,
I did simulation of two random coil peptides for 100ns.
Hi,
You can refer this paper for the topology
http://pubs.acs.org/doi/abs/10.1021/jp014476w.
---
BHARAT
On Wed, Dec 5, 2012 at 10:14 PM, James Starlight jmsstarli...@gmail.comwrote:
Dear Gromacs Users!
I'm looking for the model as well as for the pre-paired topology for
any kind
Dear gmx users,
I am planning to run REMD for a peptide (406 atoms )+ solvent system
(27639). The temperature range I selected is from 300 to 500. I want to
select appropriate temp. for 56 replicas. I randomly chose some temp
distribution and the exchange probabilities was 0.0. I know that we can
Dear gmx users,
I am planning to run REMD for a peptide (406 atoms )+ solvent system
(27639). The temperature range I selected is from 300 to 500. I want to
select appropriate temp. for 56 replicas. I randomly chose some temp
distribution and the exchange probabilities was 0.0. I know that we can
I have got the temperature distribution from the same link, but how to
select evenly spaced temperatures for 56 replicas, I need to know that
On Tue, Apr 23, 2013 at 6:21 PM, massimo sandal deviceran...@gmail.comwrote:
Look here: http://folding.bmc.uu.se/remd/
2013/4/23 bharat gupta bharat
, massimo sandal deviceran...@gmail.comwrote:
I don't understand your question. If you got the temperature distribution,
what else do you need?
2013/4/23 bharat gupta bharat.85.m...@gmail.com
I have got the temperature distribution from the same link, but how to
select evenly spaced
. There is little else you can
do, I think.
2013/4/23 bharat gupta bharat.85.m...@gmail.com
Sorry for that, I explain it again. Actually, I used the this link to
generate a temp. distribution. But I can do REMD for 56 replicas only,
as I
have 56 processors available. The t-remd calculator provides
you plan to do. I would bet on no, however.
2013/4/23 bharat gupta bharat.85.m...@gmail.com
But if I choose a smaller temperature range , would it be possible to
observe any folding event ??
On Tue, Apr 23, 2013 at 9:16 PM, massimo sandal deviceran...@gmail.com
wrote:
Thanks
with experts in these techniques, and
remember that there is no guarantee any of them will bring the result you
want. Good luck! :)
2013/4/23 bharat gupta bharat.85.m...@gmail.com
So, my final question is whether is possible to do REMD for my system,
using the computational resource that I
/MD_Simulation:_Protein_in_Water#Box_Preparationand
be sure to understand it.
2013/4/23 bharat gupta bharat.85.m...@gmail.com
Thanks a lot for your prompt responses. By using implicit solvent , I am
getting on 9 temperature values. I think this should work , I will try it
out. Also, i checked
I think it should be me who should be sorry. I should have asked the
question again in the forum without referring to some particular
individual.
On Wed, Apr 24, 2013 at 9:30 PM, massimo sandal deviceran...@gmail.comwrote:
2013/4/24 Justin Lemkul jalem...@vt.edu
I haven't said anything
Dear gmx-users,
I got the following error after issuing the final command for running 12
replicas :-
[bme:42039] *** Process received signal ***
[bme:42039] Signal: Segmentation fault (11)
[bme:42039] Signal code: Invalid permissions (2)
[bme:42039] Failing at address: 0x7f093b655340
[bme:42039]
Dear gmx members,
I performed a REMD simulation on a peptide 384 atoms (24 residues). In
total 11 replicas were simulated for a period of 50ns each. The exchange
was allwoed at every 1000 steps. The output of md.log file is :
Replica exchange statistics
Repl 24999 attempts, 12500 odd, 12499
Dear gmx members,
I have posted the same question previously , but I didn't get any reply.
So, if anyone can help me out ...
I performed a REMD simulation on a peptide 384 atoms (24 residues). In
total 11 replicas were simulated for a period of 50ns each. The exchange
was allwoed at every 1000
is not optimal and may be with regular
intervals? You want to use a exponential distribution.
On May 10, 2013, at 4:53 PM, bharat gupta bharat.85.m...@gmail.com
wrote:
Dear gmx members,
I have posted the same question previously , but I didn't get any reply.
So, if anyone can help me out ...
I
that the exchange ratio is quickly converging in the simulation so you can
make a few trials …
On May 11, 2013, at 1:40 PM, bharat gupta bharat.85.m...@gmail.com
wrote:
Dear Sir,
Thank you for your reply. I choose the temperature distribution using
t-remd calculator. Here's the link for index
… the temperature
distribution has … make some test to see how the acceptance ratio evolves …
On May 11, 2013, at 5:05 PM, bharat gupta bharat.85.m...@gmail.com
wrote:
Dear Sir,
Here's the temperature range that I got form t-remd :
1 300
2 323.7
3 348.75
4 375.23
5 403.22
6 432.83
7
Dear Sir,
I repeated the simulation again for 25 replicas with the following temp.
distribution .
280
289.1
298.5
308.2
318.2
328.6
339.3
350.3
361.7
373.5
385.6
398.1
411.1
424.4
438.3
452.5
467.2
482.4
498.1
514.3
531.0
548.3
566.1
584.5
603.5
623.2
The output of md.log file is :-
Replica
with the water …
It is not clear what happens in your index file but probably a problem
from grace to plot so many points … you can try to increase the Max
drawing path length in the preference menu of grace.
On May 13, 2013, at 4:22 PM, bharat gupta bharat.85.m...@gmail.com
wrote:
Dear Sir
affect the efficiency of REMD but
not the the exchange ratio (at least in principle).
In you case I am not sure what the plot are showing! Are these showing all
the replicas? what are the units?
On May 14, 2013, at 5:07 AM, bharat gupta bharat.85.m...@gmail.com
wrote:
Dear Sir,
Here's
between the replicas? You will
need less replicas and potentially you could run two simulations instead of
one and evaluate the convergence ...
On May 16, 2013, at 1:50 AM, bharat gupta bharat.85.m...@gmail.com
wrote:
The plots that I showed in my last mail were for all replicas. I tried
...@rug.nl wrote:
You have to convince yourself, not me :)) But I can give you my opinion …
On May 16, 2013, at 10:33 AM, bharat gupta bharat.85.m...@gmail.com
wrote:
Okay Sir, I will try two-three combinations this time and will report
back
to you ...
On Thu, May 16, 2013 at 5:25 PM
with xmgrace??
On Thu, May 16, 2013 at 5:36 PM, XAvier Periole x.peri...@rug.nl
wrote:
You have to convince yourself, not me :)) But I can give you my opinion
…
On May 16, 2013, at 10:33 AM, bharat gupta bharat.85.m...@gmail.com
wrote:
Okay Sir, I will try two-three
, Mark Abraham mark.j.abra...@gmail.comwrote:
On Thu, May 16, 2013 at 2:04 PM, bharat gupta bharat.85.m...@gmail.com
wrote:
Dear Sir,
Here's the result of three different runs :
Temperature distribution for three trials
Repeat-1 280 298 317 337 359 382 406 432 460 489 520 554 589
Dear Sir,
I ran the REMD simulation with temp. distribution discussed in my last
thread. Each replica was run for 50 ns
Replica exchange statistics
Repl 24999 attempts, 12500 odd, 12499 even
Repl average probabilities:
Repl 0123456789 10 11 12
Repl
Dear Sir,
I tried plotting the PE overlap using the following way :-
1. extract PE of each replica using g_energy
2. get the PE distribution using g_analyze -f potential_0.xvg -dist pot0.xvg
3. used xmgrace to plot all the PE distribution graphs together.
The same thing I did for temperature
of this is a work of fiction.
The number of degrees of freedom in the potential energy distribution is
also a factor in whether the distribution will look smooth for a given bin
width and number of samples.
Mark
On Fri, May 17, 2013 at 3:51 PM, bharat gupta bharat.85.m...@gmail.com
wrote:
Dear Sir
mark.j.abra...@gmail.comwrote:
On Fri, May 17, 2013 at 4:26 PM, bharat gupta bharat.85.m...@gmail.com
wrote:
Dear Sir,
The the default bin width is 0.1 which I used for plotting the graphs.
That's nice. You need to decide what you need to do about it if you want
graphs that look like those
Dear Sir,
I performed another round of trial with different set of temperature and I
got the avg accp. ration around 0.22. Here's the temp. dist. that I used :
250 268 288 308 331 355 380 408 438 469 503 540 579 621
I then checked the replica_index and replica_temp files for each replica
Hi,
I was running a simulation of 10ns which crashed in between at 1.7 ns due
to power failure. I used the following command to restart the simulation
form that point:
mdrun -s topol.tpr -cpi state.cpt -append
After checking the file md_0_1.log and others , I am getting data only for
those
Hi,
I was running a simulation of 10ns which crashed in between at 1.7 ns due
to power failure. I used the following command to restart the simulation
form that point:
mdrun -s topol.tpr -cpi state.cpt -append
After checking the file md_0_1.log and others , I am getting data only for
those
Hi,
Hi,
I have done a simulation of 10ns with my proteins and 0.5 M phosphate ion.
Now I want to know where does the phosphate ion bind on the protein surface
or distribution of phosphate ions on protein surface ?? .. can help me
finding out this
Regards
--
Bharat
--
gmx-users mailing
Yes, the phosphate ion moves around the protein but I am not able to find
out how many of them bind to my protein. How can that be done ??
On Thu, Dec 1, 2011 at 8:39 PM, Justin A. Lemkul jalem...@vt.edu wrote:
bharat gupta wrote:
Hi,
Hi,
I have done a simulation of 10ns with my
Hi,
Is there any way to get the averaged distributions of ions around the
protein surface.
On Thu, Dec 1, 2011 at 9:47 PM, Justin A. Lemkul jalem...@vt.edu wrote:
bharat gupta wrote:
Yes, the phosphate ion moves around the protein but I am not able to find
out how many of them bind to my
Hi,
I am trying the simulation of a docked complex of my protein . While
solvating the box using the following command :-
genbox -cp newbox.gro -cs spc216.gro -p topol.top -o solv.gro
The processing does not stop and continues to run . Here's the output that
I got while solvating the box ,
too large .
On Fri, Dec 2, 2011 at 10:54 AM, Justin A. Lemkul jalem...@vt.edu wrote:
bharat gupta wrote:
Hi,
I am trying the simulation of a docked complex of my protein . While
solvating the box using the following command :-
genbox -cp newbox.gro -cs spc216.gro -p topol.top -o solv.gro
the protein. Any clue what could be the reason for this ??
On Fri, Dec 2, 2011 at 11:00 AM, Justin A. Lemkul jalem...@vt.edu wrote:
bharat gupta wrote:
Actually I check the file newbox.gro in VMD and I found that the
phosphate ion instead of being docked to my protein lies somewhere far away
jalem...@vt.edu wrote:
bharat gupta wrote:
I checked the docked structure and the structure obtained after adding
the ligand coordinates to the processed file obtained after using pdb2gmx
command. It's very surprising that in the docked structure ligand is at the
correct place
Sorry to ask this , but what could be done as I don't understand how could
have happened??
On Fri, Dec 2, 2011 at 11:24 AM, Justin A. Lemkul jalem...@vt.edu wrote:
bharat gupta wrote:
Here's the coordinate of the phosphate ion from the docked complex :-
ATOM 2209 N GLY A 228
Yes, I prepared the protein file separately using pdb2gmx and then I pasted
the ligand manually from the docked file.
On Fri, Dec 2, 2011 at 11:44 AM, Justin A. Lemkul jalem...@vt.edu wrote:
bharat gupta wrote:
Sorry to ask this , but what could be done as I don't understand how
could have
Sorry I didn't understand . Can u brief it ??
On Fri, Dec 2, 2011 at 11:47 AM, Justin A. Lemkul jalem...@vt.edu wrote:
bharat gupta wrote:
Yes, I prepared the protein file separately using pdb2gmx and then I
pasted the ligand manually from the docked file.
Then you prepared
I didn't understand what you meant by that link. Can you please tell me
what can be done ??
On Fri, Dec 2, 2011 at 11:52 AM, Justin A. Lemkul jalem...@vt.edu wrote:
bharat gupta wrote:
Sorry I didn't understand . Can u brief it ??
I already did:
http://lists.gromacs.org/**pipermail/gmx
+61 3 9903 9304
-
When the only tool you own is a hammer, every problem begins to resemble a
nail.
** **
*From:* gmx-users-boun...@gromacs.org [mailto:
gmx-users-boun...@gromacs.org] *On Behalf Of *bharat gupta
*Sent:* Friday, 2 December 2011 3:22 PM
.
Ken
On Dec 30, 2011, at 6:09 PM, Justin A. Lemkul wrote:
bharat gupta wrote:
Thanks for your reply. I want to whether does it make any sense or is it
possible to simulate fragments of proteins and find their folding rate and
then correlate it to folding rate of whole protein
...
On Dec 30, 2011, at 7:04 PM, bharat gupta wrote:
Thanks for your advice... Could you please refer me some papers regarding
this
On Sat, Dec 31, 2011 at 8:17 AM, KS Rotondi k...@chemistry.umass.eduwrote:
No, there is no way to use such data to determine the folding rate of
the intact
, bharat gupta wrote:
Thanks for your advice... Could you please refer me some papers
regarding this
On Sat, Dec 31, 2011 at 8:17 AM, KS Rotondi k...@chemistry.umass.eduwrote:
No, there is no way to use such data to determine the folding rate of
the intact protein. If you used a fragment
in MDS that could be used ??
On Wed, Jan 4, 2012 at 10:52 AM, Mark Abraham mark.abra...@anu.edu.auwrote:
On 4/01/2012 12:35 PM, bharat gupta wrote:
Thanks for all your replies. I want to know this can be done in gromacs
or not - using REMD with structure based models generated from SMOG server
Hi,
I am trying to run a REMD of a peptide. But while executing the following
command after nvt and npt equilibration , I am getting the following error:-
mdrun_mpi mdrun -s prefix_.tpr -multi 20 -replex 1000
mdrun_mpi: error while loading shared libraries: libgmx_mpi.so.6: cannot
enable
AM, bharat gupta wrote:
Hi,
I am trying to run a REMD of a peptide. But while executing the
following command after nvt and npt equilibration , I am getting the
following error:-
mdrun_mpi mdrun -s prefix_.tpr -multi 20 -replex 1000
mdrun_mpi: error while loading shared libraries
On Thu, Jan 12, 2012 at 3:53 PM, Mark Abraham mark.abra...@anu.edu.auwrote:
On 12/01/2012 5:45 PM, bharat gupta wrote:
It says that The number of cores must be a multiple of the number of
replicas (given with -multi, which must equal the number of
.tprhttp://www.gromacs.org/Documentation
Hi,
I have been trying to attach the chromophore of GFP in charmm ff parameter
files. The parameters have been obtained from a published article. After
making the changes as per the documentation (
http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field)
, I am getting
Hi,
I am planning to carry out a REMD study on a 12 residue beta-hairpin
peptide. I have read the gromacs tutorial for that . I have certain doubts
regarding the tutorial :-
1. Step. 4 says that run short simulations to have an estimate of the
exchange rate (can get a good estimate within ~100
Hi,
I am trying to plot the ss content using the do_dssp command , but I am
getting the following error :-
Failed to execute command: /usr/local/bin/dsspcmbi -na ddldj5Bn ddXN9mH0
/dev/null 2 /dev/null
I am using the DSSPold version. What could be the possible reason for such
an error ??
Yes , I am using the correct options for dssp. But still I am getting the
same error.
On Thu, Apr 5, 2012 at 2:12 PM, Mark Abraham mark.abra...@anu.edu.auwrote:
On 5/04/2012 10:25 AM, bharat gupta wrote:
Hi,
I am trying to plot the ss content using the do_dssp command , but I am
getting
Abraham mark.abra...@anu.edu.auwrote:
On 5/04/2012 4:16 PM, bharat gupta wrote:
Yes , I am using the correct options for dssp. But still I am getting the
same error.
What does invoking /usr/local/bin/dsspcmbi say?
Mark
On Thu, Apr 5, 2012 at 2:12 PM, Mark Abraham mark.abra
1crn.dssp, you type:
dssp.exe -i 1crn.pdb -o 1crn.dssp
On Thu, Apr 5, 2012 at 4:23 PM, Mark Abraham mark.abra...@anu.edu.auwrote:
On 5/04/2012 5:16 PM, bharat gupta wrote:
*This is the output :
[root@BHARATPC ~]# /usr/local/bin/dssp
*
Don't run as root except for installing
You can use g_saltbr option , http://manual.gromacs.org/online/g_saltbr.html
On Thu, Apr 5, 2012 at 5:23 PM, James Starlight jmsstarli...@gmail.comwrote:
Dear Gromacs Users!
I'd like to monitor origin and destabilisation of salt-bridges during
simulation time. In particular I want to define
Hi,
I am trying to enable mpi fro mdrun in an already installed gromacs-4.5.5.
But while executing the command make mdrun , I am getting the following
errorn:-
mv -f .deps/xlate.Tpo .deps/xlate.Plo
/bin/sh ../../libtool --tag=CC --mode=link mpicc -O3
-fomit-frame-pointer -finline-functions
Hi all,
I have recently started working with GROMACS , and I am not able to
find xmgrace in GROMACS folder . Do I have to download the file
separately ??
Thanks
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
Hi all,
I have recently started working with GROMACS , and I am not able to
find xmgrace in GROMACS folder . Do I have to download the file
separately ??
--
Bharat
M.Sc. Bioinformatics (Final year)
Centre for Bioinformatics
Pondicherry University
Puducherry
India
Mob. +919962670525
--
Thanks sir
But there is one problem that when I am running the mdrun step of 5th
step of lysozyme tutorial, I am getting an error :-
Can not open file:
topol.tpr
Can u tell me how to rectify it ..
--
gmx-users mailing listgmx-users@gromacs.org
hi all,
I am trying to install xmgrace on redhat linux 5 and I am getting the
following two errors after running the ./configure command :-
checking for a Motif = 1002 compatible API... no
configure: error: M*tif has not been found
Can u pls tell how can I rectify the error .. or shall I go
Sir
I am installing openMotif-2.2.3 version but after make command I
getting the follwoing error :-
In file included from XmStrDefs.c:10:
../Xm/Xm.h:59:34: error: X11/extensions/Print.h: No such file or directory
In file included from XmStrDefs.c:10:
../Xm/Xm.h:827: error: expected
Hi all
Can anybody tell me which version of GRACE shall i install for red hat
linux 5 since i am getting errors after compilation ??
--
Bharat
M.Sc. Bioinformatics (Final year)
Centre for Bioinformatics
Pondicherry University
Puducherry
India
Mob. +919962670525
--
gmx-users mailing list
Hi
I am getting the follwing error while running the mdrun command given
in the step six of the lysozyme tutorial :-
Program mdrun, VERSION 4.0.7
Source code file: gmxfio.c, line: 737
Can not open file:
topol.tpr
---
This Doesn't Suck, It's
here is the link for that tutorial ...
and one more thing I wanna ask that in the tutorial he has asked to
download to .mdp file (like ions.mdp) . My doubt is .. I should know
the theory for creating such files for the system of my study ..
Bharat
--
gmx-users mailing list
thanks for the advice sir ..
Actually I have to study how the interaction between a coiled peptide
and a protein takes place through simulation .. and i am new to
simulation .. i know a little theory about simulation .. so can u
suggest me how to start ... and will it possible to complete my
hi all,
Can anyboddy tell me from where I can get full detail of MPI with
respect to GROMACS ..
--
Bharat
M.Sc. Bioinformatics (Final year)
Centre for Bioinformatics
Pondicherry University
Puducherry
India
Mob. +919962670525
--
gmx-users mailing listgmx-users@gromacs.org
Hi all,
This is a general question I wanna ask about deposition of sequences
in NCBI or UNIPROT :-
The sequence that is displayed in NCBI or UNIPROT starts from either
the N terminus or the C- terminus ???
--
Bharat
M.Sc. Bioinformatics (Final year)
Centre for Bioinformatics
Pondicherry
Hi all,
I have modelled a structure and I want to minimize it using GROMACS
but while generating the topology file using pdb2gmx command I am
getting the following error :-
Atom HN1 in residue LEU 1 not found in rtp entry with 9 atoms
while sorting atoms. Maybe different protonation
Thanks for the help mdrun step is going on now .. but I wanna ask one
thing that how can I visualize the minimized structure .. The
structure which I used initially is the minimized structure or not ??
Bharat
M.Sc. Bioinformatics (Final year)
Centre for Bioinformatics
Pondicherry University
Hi all,
I had followed all the 7 steps of gromacs beginners tutorial and I
have a doubt that during the minimization step .. which structure is
minimized one ?? The one that i used for the minimization step ...
Pls reply
--
Bharat
M.Sc. Bioinformatics (Final year)
Centre for Bioinformatics
Hi all,
I am trying to save the conformation of my protein after 10ps
simulation .. I am getting the following error :-
Software inconsistency error:
Not supported in write_sto_conf
Can anybody tell me how to fix this error ..
--
Bharat
M.Sc. Bioinformatics (Final year)
Centre for
Hi all
I wanna know that for how long shall I run the energy minimization
step to minimize my modelled protein structure .. and what all
parameters shall I look for the minimized structure - rms , rmsf ,
potential , g_energy . In g_energy total energy and potential both
have to be checked ...
--
so how shall i proceed now ... can u guide ??
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www
Hi all,
I am interested in Protein - Carbohydrate interaction study using
dynamics .. Is it possible through GROMACS .. Can anybody refer me to
some papers for that .. or any help in this area ...
Pls reply
--
Bharat
M.Sc. Bioinformatics (Final year)
Centre for Bioinformatics
Pondicherry
Hi all,
I am interested in studying the interactions between the Sulf2 protein
(endosulfatase) , which I have modelled and its substrate hearan
sulfate . Can anybody help me to carry out such type of simulation
studies ..
Please reply ASAP
--
Bharat
M.Sc. Bioinformatics (Final year)
Centre for
Hi all
I have modeled a structure with the active site residue as a
heteroatom (formyl glycine) and when I am minimizing the structure
gromacs is giving error that it cannot minimize it .. can anybody tell
me how can i minimize it ...
thanks
--
Bharat
M.Sc. Bioinformatics (Final year)
Centre
Hi all,
I have modelled a protein with one residue as formylated glycine which
is the active site residue of my protein and when I am running the
pdb2gmx command I am getting the following error :-
Back Off! I just backed up npep.top to ./#npep.top.4#
Processing chain 1 (2862 atoms, 358
Sir ,
I have read both the files description but to create such files I need
all the bond angles , dihedral angles , connectivity but I don't know
from where I can get such informations about my molecule ..
--
Bharat
M.Sc. Bioinformatics (Final year)
Centre for Bioinformatics
Pondicherry
Hi all ,
I have performed a 3ns simulation and after that I have found that the
protein has moved out of the simulation box. Can anybody tell how can
I fix this problem without performing the simulation again ..
Thanks
--
Bharat
M.Sc. Bioinformatics (Final year)
Centre for Bioinformatics
Hi,
I want to dock a barrel protein with phosphate ion , to look for the sites
where Phosphate ion binds... I searched the gmx list but I didn't find much
related threads..
I want to do the following things...
1) Simulate the binding of phosphate ion with a barrel protein. Here I do
not know
with phosphate ion, can I use MD for checking how strong the
binding is or does the ion tries to move inside the barrel.
On Mon, May 30, 2011 at 4:19 PM, Justin A. Lemkul jalem...@vt.edu wrote:
bharat gupta wrote:
Hi,
I want to dock a barrel protein with phosphate ion , to look for the sites
where
in my case. I
don't want them to enter the barrel rather I want them to be on the surface
of the barrel??
On Mon, May 30, 2011 at 4:48 PM, Justin A. Lemkul jalem...@vt.edu wrote:
bharat gupta wrote:
Thanks for your reply..
Actually I came across a paper Molecular Modeling of the RNA binding
Well, mine is a beta-barrel protein called Green Fluorescent Protein. In
such a case the movement of ion is very important. As the ion in side the
barrel can quench the fluorescence. That's what I want to track..
On Mon, May 30, 2011 at 4:57 PM, Justin A. Lemkul jalem...@vt.edu wrote:
bharat
thanks ...
On Mon, May 30, 2011 at 5:03 PM, Justin A. Lemkul jalem...@vt.edu wrote:
bharat gupta wrote:
Well, mine is a beta-barrel protein called Green Fluorescent Protein. In
such a case the movement of ion is very important. As the ion in side the
barrel can quench the fluorescence
bharat,
you can try Phosfinder (http://phosfinder.bio.uniroma2.it). It is a
website that predict phosphate binding site on protein stucture.
The paper url is: http://www.ncbi.nlm.nih.gov/pubmed/21622655
Il 31/05/2011 02:06, bharat gupta ha scritto:
thanks ...
On Mon, May 30, 2011 at 5:03 PM
Hi,
I want to know is there any well documented tutorial for SMD in gromacs ??
--
Bharat
Ph.D. Candidate
Room No. : 7202A, 2nd Floor
Biomolecular Engineering Laboratory
Division of Chemical Engineering and Polymer Science
Pusan National University
Busan -609735
South Korea
Lab phone no. -
Hi Justin,
I am having following doubts regarding umbrella sampling of phosphate ion
binding to my protein .
1. As per the tutorial, I need to fix an immobile reference. In my case
which region do I have to fix as my protein consists of one single chain.
Since I am studying the binding and
:
bharat gupta wrote:
Hi Justin,
I am having following doubts regarding umbrella sampling of phosphate ion
binding to my protein .
1. As per the tutorial, I need to fix an immobile reference. In my case
which region do I have to fix as my protein consists of one single chain.
Since I am
1 5 1 1.082000e+02
7 2 5 1 1.082000e+02
[ dihedrals ]
; aiajakal funct
6 1 5 2 1
7 2 5 1 1
Can I use it or not ??
On Thu, Jun 9, 2011 at 10:26 AM, Justin A. Lemkul jalem...@vt.edu wrote:
bharat gupta wrote:
does
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