/11/13 6:56 PM, bharat gupta wrote:
>
>> Hi,
>>
>> I tried g_select to dump the structure with the interacting water
>> molecules, but I don't know know how to do that. I searched for some
>> threads in the discussion but wasn't able to find anything
ydrogen
> bonds are formed during the simulation time of 5ns to 10ns. What does then
> the average file or its graph tells ??
>
>
>
> On Mon, Nov 11, 2013 at 9:58 PM, Justin Lemkul wrote:
>
>>
>>
>> On 11/11/13 4:06 AM, bharat gupta wrote:
>>
>>>
. What does then
the average file or its graph tells ??
On Mon, Nov 11, 2013 at 9:58 PM, Justin Lemkul wrote:
>
>
> On 11/11/13 4:06 AM, bharat gupta wrote:
>
>> In addition to my previous question, I have another question about
>> g_analyze. When I used the hbond.xv
the link hbond.xvg file and its averaged file
https://www.dropbox.com/s/4n0m47o3mrjn3o8/hbond_115-water.xvg
https://www.dropbox.com/s/4n0m47o3mrjn3o8/hbond_115-water.xvg
On Mon, Nov 11, 2013 at 3:30 PM, bharat gupta wrote:
> thank you informing about g_rdf...
>
> Is it possible to dump
:
>
>
> On 11/10/13 8:38 PM, bharat gupta wrote:
>
>> But trjorder can be used to calculate the hydration layer or shell around
>> residues ... Right ??
>>
>>
> Yes, but I also tend to think that integrating an RDF is also a more
> straightforward way o
But trjorder can be used to calculate the hydration layer or shell around
residues ... Right ??
On Mon, Nov 11, 2013 at 10:35 AM, Justin Lemkul wrote:
>
>
> On 11/10/13 8:30 PM, bharat gupta wrote:
>
>> Thanks for your reply. I was missing the scientific notation part. No
Thanks for your reply. I was missing the scientific notation part. Now
everything is fine.
Regarding trjorder, it doesn't measure h-bonds but gives the water nearest
to protein.
On Mon, Nov 11, 2013 at 10:12 AM, Justin Lemkul wrote:
>
>
> On 11/10/13 7:18 PM, bharat gupta
hanks
---
BHARAT
On Sun, Nov 10, 2013 at 10:01 PM, Justin Lemkul wrote:
>
>
> On 11/10/13 12:20 AM, bharat gupta wrote:
>
>> Hi,
>> I used the command g_hbond to find h-bond between residues 115-118 and
>> water. Then I used g_analyze to find out the average a
Hi,
I used the command g_hbond to find h-bond between residues 115-118 and
water. Then I used g_analyze to find out the average and it gives the value
for the hbonds like this :-
std. dev.relative deviation of
standard -
Hi,
I am getting the following error while using the command -
[root@localhost INGT]# mpirun -np 24 mdrun_mpi -v -deffnm npt
Error -
/usr/bin/mpdroot: open failed for root's mpd conf
filempiexec_localhost.localdomain (__init__ 1208): forked process failed;
status=255
I complied gromacs using -
Hi,
I have installed Gromcas 4.5.6 on Rocks cluster 6.0 andmy systme is having
32 processors (cpu). But while running the nvt equilibration step, it uses
only 1 cpu and the others remain idle. I have complied the Gromacs using
enable-mpi option. How can make the mdrun use all the 32 processors ??
Hi,
I have installed Gromcas 4.5.6 on Rocks cluster 6.0 andmy systme is having
32 processors (cpu). But while running the nvt equilibration step, it uses
only 1 cpu and the others remain idle. I have complied the Gromacs using
enable-mpi option. How can make the mdrun use all the 32 processors ??
Hi,
I am trying to install gromacs 4.5.7 on rocks cluster(6.0) and it works
fine till .configure command, but I am getting error at the make command :-
Error:
[root@cluster gromacs-4.5.7]# make
/bin/sh ./config.status --recheck
running CONFIG_SHELL=/bin/sh /bin/sh ./configure
Hi,
I want to know the exact way to calculate the density of water around
certain residues in my protein. I tried to calculate this by using
g_select, with the following command :-
g_select -f nvt.trr -s nvt.tpr -select "Nearby water" resname SOL and
within 0.5 of resnr 115 to 118 -os water.xvg
Hi,
I am trying to install gromacs 4.5.7 on rocks cluster(6.0) and it works
fine till .configure command, but I am getting error at the make command :-
Error:
[root@cluster gromacs-4.5.7]# make
/bin/sh ./config.status --recheck
running CONFIG_SHELL=/bin/sh /bin/sh ./configure
Hi,
I want to know the exact way to calculate the density of water around
certain residues in my protein. I tried to calculate this by using
g_select, with the following command :-
g_select -f nvt.trr -s nvt.tpr -select "Nearby water" resname SOL and
within 0.5 of resnr 115 to 118 -os water.xvg
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/03_solvate.html
On Mon, Aug 12, 2013 at 4:09 PM, wrote:
> Hi
>
> I want to add water molecule in my structure. Do anyone have idea how to
> add water molecules in protein structure. I little aware of python.
> How t
e wole tale, but is it possible you
> are running xmgrace without the -nxy option?
> You are probably visualizing the data related the 1st replica several
> times!
>
> Francesco
>
>
> 2013/5/24 Mark Abraham
>
> > On Fri, May 24, 2013 at 10:44 AM, bharat gupta > &g
> at which time.
>
> Mark
>
>
> On Fri, May 24, 2013 at 8:43 AM, bharat gupta >wrote:
>
> > Dear Sir,
> >
> > I tried a lot to understand the meaning and relation between the .log
> file
> > and relica_index file, but I was not able to break the cod
789 10 11 13
12
On Thu, May 23, 2013 at 11:20 PM, Mark Abraham wrote:
> Looked fine
>
>
> On Thu, May 23, 2013 at 4:13 PM, bharat gupta >wrote:
>
> > Sir,
> >
> > What about the description of replica_temp file that I posted in last
> mail.
&g
Sir,
What about the description of replica_temp file that I posted in last mail.
I think that's correct ... If you can comment on that, I can move on with
replica_index file...
On Thu, May 23, 2013 at 10:58 PM, Mark Abraham wrote:
> It's a demux. One might want trajectories to be at constant te
tion
> from each .log file.
>
> Mark
>
>
> On Thu, May 23, 2013 at 9:01 AM, bharat gupta >wrote:
>
> > I checked the first 5 md.log files, and the data is exactly the same in
> all
> > of them Does it mean there could be problem with demux.pl
> >
g the first column of each. You want to look at each
> column. (And even then the best it can show is that your simulation is not
> clearly inadequate.)
>
> Mark
>
>
> On Thu, May 23, 2013 at 8:48 AM, bharat gupta >wrote:
>
> > Dear Sir,
> >
> > Thank you
Dear Sir,
Thank you for your reply. But I used the command demux.pl md$.log , where
$= No. of replica. I get the same plot every time. Sorry to ask this , but
where am I going wrong ??
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please
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
individu
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
individu
:
> On Fri, May 17, 2013 at 4:26 PM, bharat gupta >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
s 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 >wrote:
&
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 dis
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
t 11:24 PM, Mark Abraham wrote:
> On Thu, May 16, 2013 at 2:04 PM, bharat gupta >wrote:
>
> > Dear Sir,
> >
> > Here's the result of three different runs :
> >
> > Temperature distribution for three trials
> >
> > Repeat-1 280 298 317 337 359
Okay, now I can start with large production runs .
On Thu, May 16, 2013 at 11:10 PM, XAvier Periole wrote:
>
> Indeed the Repeat-3 seems good. But I would guess you did not run too
> long, right! That would explain the distribution of values!
>
> On May 16, 2013, at 2:04 P
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
> wrote:
>
> > Okay Sir, I will try two-three combinations this time and will report
> back
> > to you ...
> >
> >
> >
you just increase the spacing 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
> wrote:
>
> > The plots that I showed in my last mail
ct 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
> wrote:
>
> > Dear Sir,
> >
work 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
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 exc
not importance … the temperature
> distribution has … make some test to see how the acceptance ratio evolves …
>
> On May 11, 2013, at 5:05 PM, bharat gupta
> wrote:
>
> > Dear Sir,
> >
> > Here's the temperature range that I got form t-remd :
> > 1 300
you need. Note
> 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
> wrote:
>
> > Dear Sir,
> >
> > Thank you for your reply. I choose the temperature distributio
emperature 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
> wrote:
>
> > Dear gmx members,
> >
> > I have posted the same question previously , but I didn't get any
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 st
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 even
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]
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 wrote:
> 2013/4/24 Justin Lemkul
>
> >
> >
> > I haven't said anything because I agree with what Mass
other. See
>
> http://ringo.ams.sunysb.edu/index.php/MD_Simulation:_Protein_in_Water#Box_Preparationand
> be sure to understand it.
>
>
> 2013/4/23 bharat gupta
>
> > Thanks a lot for your prompt responses. By using implicit solvent , I am
> > getting on 9 temperature values.
l* this kind of things, talk 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
>
> > So, my final question is whether is possible to do REMD for my s
do. I would bet on "no", however.
>
>
> 2013/4/23 bharat gupta
>
> > 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 > >wrote
ose a smaller temperature range. There is little else you can
> do, I think.
>
>
> 2013/4/23 bharat gupta
>
> > 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
> &
, massimo sandal wrote:
> I don't understand your question. If you got the temperature distribution,
> what else do you need?
>
>
> 2013/4/23 bharat gupta
>
> > I have got the temperature distribution from the same link, but how to
> > select evenly spaced temp
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 wrote:
> Look here: http://folding.bmc.uu.se/remd/
>
>
>
> 2013/4/23 bharat gupta
>
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
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 wrote:
> Dear Gromacs Users!
>
>
> I'm looking for the model as well as for the pre-paired topology for
> any kind of GFP protein with
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 wrote:
> Hi Gromacs Users,
>
>I did simulation of two random coil peptides for 100ns.
> after 70 ns these peptide
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 tim
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
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 wrote:
> Sorry
ethod
would be useful ??
On Thu, Jun 14, 2012 at 4:16 PM, Mark Abraham wrote:
> 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.
>
>
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 wrote:
> On 14/06/2012 4:38 PM, bharat gupta wrote:
>
> Thanks Sir for the reply... This question is related to my first query
> that if we co
particular
phi psi angle range
On Thu, Jun 14, 2012 at 11:21 AM, Mark Abraham wrote:
> 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 c
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 wrote:
>
>
> On 6/13/12 9:44 PM, bharat gupta wrote:
>
>> Hi,
>>
>> I wanted to simulate a
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
http://lists.g
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 -Wal
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 wrote:
> Dear Gromacs Users!
>
>
> I'd like to monitor origin and destabilisation of salt-bridges during
> simulation time. In particular I want to define some charged resi
ile called 1crn.dssp, you type:
dssp.exe -i 1crn.pdb -o 1crn.dssp
On Thu, Apr 5, 2012 at 4:23 PM, Mark Abraham wrote:
> 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
Mark Abraham wrote:
> 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 P
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 wrote:
> 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
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 ??
Re
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 p
51?
>
> Can you generate a correct topology without the chromophore as a check?
>
> On 2012-01-19 11:50:37AM +0900, bharat gupta wrote:
> > Hi,
> >
> > I have been trying to attach the chromophore of GFP in charmm ff
> parameter
> > files. The parameters h
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 follo
MM_WORLD, -1) - process 0
On Thu, Jan 12, 2012 at 3:53 PM, Mark Abraham wrote:
> 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
> .tpr<h
refix_9.tpr)"
I gave the options -multi 5 . But still I am getting the same error. Can
you please explain, why is it so. Do I need to have the same no. of cores
as the no. of .tpr files ??
On Thu, Jan 12, 2012 at 3:38 PM, Mark Abraham wrote:
> On 12/01/2012 5:29 PM, bharat gupta wrote:
ng program mdrun_mpi
gcq#155: "BioBeat is Not Available In Regular Shops" (P.J. Meulenhoff)
application called MPI_Abort(MPI_COMM_WORLD, -1) - process 0
I am trying to simulate 5 replicas and I have 4 cpu .
On Thu, Jan 12, 2012 at 1:37 PM, lina wrote:
> On Thursday 12,January,2012
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 executab
MDS that could be used ??
On Wed, Jan 4, 2012 at 10:52 AM, Mark Abraham wrote:
> 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
&
ce.1208351
>>
>> Regards,
>> João
>>
>> On Sat, Dec 31, 2011 at 12:19 AM, KS Rotondi wrote:
>>
>>> As Justin pointed out, there is a vast literature on this topic, you
>>> need to ask yourself what you seek, and look at many review articles to
>&
u seek, and look at many review articles to
>> find some reasonable starting points for you own needs and designs. Beyond
>> that, it's a lot of hard work...
>>
>> On Dec 30, 2011, at 7:04 PM, bharat gupta wrote:
>>
>> Thanks for your advice... Could you ple
.
>
> 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 th
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 Sat, Dec 31, 2011 at 8:00 AM, Justin A. Lemkul wrote:
>
>
> bharat gupta wrote
Hi,
I want to know whether it's possible to calculate the folding rate of 20
residue peptide folding into a beta-hairpin using gromacs ??
--
Bharat
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gro
yal Parade, Parkville VIC 3010
> dallas.war...@monash.edu
>
> +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-use
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 wrote:
>
>
> bharat gupta wrote:
>
>> Sorry I didn't understand . Can u brief it ??
>>
>>
> I already did:
&
Sorry I didn't understand . Can u brief it ??
On Fri, Dec 2, 2011 at 11:47 AM, Justin A. Lemkul wrote:
>
>
> bharat gupta wrote:
>
>> Yes, I prepared the protein file separately using pdb2gmx and then I
>> pasted the ligand manually from the docked file.
>>
&
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 wrote:
>
>
> bharat gupta wrote:
>
>> Sorry to ask this , but what could be done as I don't under
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 wrote:
>
>
> bharat gupta wrote:
>
>> Here's the coordinate of the phosphate ion from the docked complex :-
>> ATOM
A. Lemkul 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 struct
from
the protein. Any clue what could be the reason for this ??
On Fri, Dec 2, 2011 at 11:00 AM, Justin A. Lemkul 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 li
being
too large .
On Fri, Dec 2, 2011 at 10:54 AM, Justin A. Lemkul 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 new
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 , which
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 wrote:
>
>
> bharat gupta wrote:
>
>> Yes, the phosphate ion moves around the protein but I am not able to find
>> out how many of
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 wrote:
>
>
> bharat gupta wrote:
>
>> Hi,
>>
>> Hi,
>>
>> I have
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 li
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 1.7
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 1.7
010
> dallas.war...@monash.edu
>
> +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...@gromac
> 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: Wednesday, 28 September 2011 12:48 PM
> To: jalem...@vt.edu; Disc
ions as I have
simulated my protein in water earlier without any problem. During nvt
quilibration the temperature coupling settings were for Protein and Non
protein groups. Do I have to make groups for Protein and water_ion. Please
comment??
On Tue, Sep 27, 2011 at 7:09 PM, Justin A. Lemkul wrote
HI,
I have tried simulating my protein (GFP) solvated with water molecules and
10 phosphate ions. During the md run step the system starts exploding after
500 ps. What could be the reason for this . I know this is happening due to
the addition of phosphate ion but I need to study the binding of i
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