Hi everyone
This may be irrelevant to the list but i have a big problem. I have
designed some inhibitors using molecular docking and then performed 10 nsmd
simulations. I have to submit the article for publication. But the journal
is asking for the names of persons to review the article. Can you
ok thanks i'll try this
Regards
On Mon, Apr 29, 2019 at 5:23 AM Justin Lemkul wrote:
>
>
> On 4/25/19 8:49 AM, neelam wafa wrote:
> > Hi!
> > I have run 5ns simulation of protein ligand complex and got its rmsd plot
> > using gmx_rms. How can i get average rms
Ok i ll try
Thanks
On Mon, 29 Apr 2019, 7:06 am Neena Susan Eappen, <
neena.susaneap...@mail.utoronto.ca> wrote:
> Hi Neelam,
>
> I do not have Xmgrace tool, but you can open up the xvg file on excel and
> calculate average.
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> Gromacs Users mailing list
>
> * Please search the archive at
>
> energies of binding can be usefully made.
>
> Mark
>
> On Sat., 20 Apr. 2019, 14:17 neelam wafa, wrote:
>
> > Hi!
> > Dear Sir Justin.
> > I have run 5 ns simulations of two different enzymes in unbound form and
> in
> > complex with 4 different inhibit
of such matters.Thanks in advance.
Regards
Neelam Wafa
Ph. D scholar
University of the Punjab Lahore, Pakistan
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ecution: less than a second
> >
> > Looking forward for your suggestions
> > Regards
> >
> > On Thu, Nov 1, 2018 at 10:05 PM Alan wrote:
> >
> > > Please, post here the command you're using (add -d anyway for debug)
> and
> > > show the whol
FAILED: [Errno 2] No such file or directory: 'tmp'
Total time of execution: less than a second
Regards
On Fri, Nov 2, 2018 at 7:02 PM neelam wafa wrote:
> Hi!
> This is the command I use
> dr@dr-HP-1000-Notebook-PC:~/Downloads/acpype/test$ ../acpype.py -di
> H16.mol2 -c gas
>
gt; Please, post here the command you're using (add -d anyway for debug) and
> show the whole output.
>
> Thanks,
>
> Alan
>
> On Thu, 1 Nov 2018 at 20:04, neelam wafa wrote:
>
> > Yes it the same one. And the tests are running okay. Problem is with my
> > files.
YPE?
>
>
>
> | ACPYPE: AnteChamber PYthon Parser interfacE v. 2018-09-20T16:44:17UTC (c)
> 2018 AWSdS |
>
>
>
>
> On Thu, 1 Nov 2018 at 19:46, neelam wafa wrote:
>
> >
t; (3) increase PSCUTOFF in define.h and recompile bondtype.c
> Be cautious, use a large value of PSCUTOFF (>100) will significantly
> increase the computation time
>
>
> On Thu, 1 Nov 2018 at 08:53, neelam wafa wrote:
>
> > Hi!
> > Dear all
> > I am using acpype to
before commanding acpype for the conversion?
> Apparently it’s looking for antechamber but it can’t access it.
> When amber is sourced first, you can get a result from commands such as
> antechamber -h
> Try to first source your amber, and then run acpype.
>
> > On 1 Nov 2018,
Hi!
Dear all
I am using acpype to generate topologies of ligand for gromacs md
simmulation. I habe amber tools 18 and downloaded acpype from github. The
test runs go well but when i run my file with ../acpype.py -i UNL.mol2 -c
gas or even
../acpype.py -di UNL.mol2
iI get following error
Hi
I am using acpype . I have amber tools 18. I get an error. When I run my
ligand file for topology i got ACPYPE failed: Errno 2 no such file or
directory: 'temp'.
Any suggestion for the problem . Thanks in advance.
Regards
Show quoted text
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I have by defalt python 2.7.6
and python 3.4.3
Regards
On Tue, 30 Oct 2018, 1:11 am Alan, wrote:
> Are you running python3?
>
> what
>
> python -V
>
> or
>
> python3 -V
>
> outputs?
>
> Alan
>
> On Mon, 29 Oct 2018 at 13:25, neelam wafa wro
If your default python is already python3,
> then change line to
>
> #!/usr/bin/env python
>
> python -V
>
> tells which python version you have.
>
> Thanks,
>
> Alan
>
> On Thu, 25 Oct 2018 at 16:44, neelam wafa wrote:
>
> > Hi, Alan
> >
>
n't tell you exactly because we need several
> tests. It's a complete new version re-written from scratch.
>
> I'm really sorry for the inconvenience but we hope to bring it back in a
> month or two.
>
> Alan
>
> On Wed, 24 Oct 2018 at 16:58, neelam wafa wrote:
>
> >
Hi alan
Can you please tell how long will it take for the online acpype server to
be available?
Regards
Neelam wafa
On Wed, 24 Oct 2018, 6:23 pm Alan, wrote:
> Indeed, it's mostly Luciano spearheading these new things. Hopefully, we
> will have more things to show eventually.
&g
Hi !
Alan the link for updated acpype you have shared is all about the
downloadable tool. Can you please share the link for online server for
it. and is their any tutorial to explain the changed protocol.
looking forward for your cooperation.
Regards
On 9/20/18, Alan wrote:
> Please, official,
Sir Justin and sir Mark
Please comment on my question. I ll be really thankful to you.
On Tue, 28 Aug 2018, 11:07 pm neelam wafa, wrote:
> Hi gmx users,
> I want to calculate free energy of binding for protein ligand complex. In
> first step of free energy of solvation when i have
Hi gmx users,
I want to calculate free energy of binding for protein ligand complex. In
first step of free energy of solvation when i have to create lambda states
vwd_lambda changes from 0.00 and increases gradually to 1. Can the
coul_lambda be changed fradually after the vwd_lambda becomes 1.
Hi everyone.
Kindlt need your help urgently.
-- Forwarded message -
From: neelam wafa
Date: Mon, 27 Aug 2018, 3:41 pm
Subject: free energy calculation.
To: ,
Hi!
Dear gmx users,
I have md simmulations of a protein with four different ligands. now I want
to calculate the free
Hi!
Dear gmx users,
I have md simmulations of a protein with four different ligands. now I want
to calculate the free energy of binding. which method does suit after md
simmulation? either g_mmpbsa or gmx BAR method. If I use BAR method is
it necessary to set charges to zero as in the tutorial
?
Looking forward for your valuable suggestions.
Regards
On Wed, Jul 18, 2018 at 5:42 PM, neelam wafa wrote:
> Thanks sir Mark,
>
> I have compared the complex before and after the minimization. there are
> slight differences in the bond angles and interactions. overall posture i
-- Forwarded message --
From: neelam wafa
Date: Tue, Jul 17, 2018 at 1:12 PM
Subject: problem in energy minimization
To: gromacs.org_gmx-users@maillist.sys.kth.se
Hi,
Dear gromacs users, I am running md simmulation of a protein with a ligand.
i have already done
Hi,
Dear gromacs users, I am running md simmulation of a protein with a ligand.
i have already done it with the same protein and a different ligand. Now
when i run em md run i get following result.
Energy minimization has stopped, but the forces have not converged to the
requested precision Fmax
Dear gmx users!
I am running md simmulation of a protein with different ligands but the
speed is decreasing with every simmulation. In first one it was 25hrs/ns,
for second one it became 35 hrs/ns then 36hs/ns. what can be the reason?
I am using this command for the run.
How to select the value
same folder, too :-D
>
> Mark
>
> On Fri, May 11, 2018, 21:01 Justin Lemkul <jalem...@vt.edu> wrote:
>
> >
> >
> > On 5/11/18 2:11 PM, neelam wafa wrote:
> > > Hi!
> > > does this means that i should not have used -deffnm md_0_1 in the run
>
e too...
>
> Mark
>
> On Fri, May 11, 2018 at 7:28 PM neelam wafa <neelam.w...@gmail.com> wrote:
>
> > okay,
> >
> > Thanks
> >
> > On Fri, May 11, 2018 at 5:19 PM, Justin Lemkul <jalem...@vt.edu> wrote:
> >
> > >
> > >
okay,
Thanks
On Fri, May 11, 2018 at 5:19 PM, Justin Lemkul <jalem...@vt.edu> wrote:
>
>
> On 5/11/18 1:18 PM, neelam wafa wrote:
>
>> *This is the message of gmx check for both the trajectories. I*t means
>> that
>> trajectory is not continuous. Am I right
(nm)
Last frame 13 time 2850.000
Item#frames Timestep (ps)
Step1410
Time1410
Lambda 0
Coords 1410
Velocities 0
Forces 0
Box 1410
On Fri, May 11, 2018 at 5:12 PM, neelam wafa <neela
The previous command was :
gmx mdrun -deffnm md_0_1
I didn't ust -cpi falg .
On Fri, May 11, 2018 at 5:01 PM, Justin Lemkul <jalem...@vt.edu> wrote:
>
>
> On 5/11/18 12:52 PM, neelam wafa wrote:
>
>> I used this command:
>> gmx mdrun -s md_0_1.tpr -cpi md
files but not able to infer a
proper answer.
If its not appened, will the final trajectory .xtc obtained cover the whole
simmulation or I ll have to combine both results?
Regards
On Fri, May 11, 2018 at 2:49 PM, Justin Lemkul <jalem...@vt.edu> wrote:
>
>
> On 5/11/18 10:42 AM, ne
Dear Sir Justin!
I have restarted the simmulation but its producing a separate log file
starting from the step where restarted. Is it normal response or there is
some problem with my restart?
Thanks in advance.
On Fri, May 11, 2018 at 12:06 PM, neelam wafa <neelam.w...@gmail.com>
Thanks Sir Justin!
I have continued the simmulation from the last step.
Regards
On Thu, May 10, 2018 at 12:08 PM, Justin Lemkul <jalem...@vt.edu> wrote:
>
>
> On 5/10/18 7:08 AM, neelam wafa wrote:
>
>> Hi gmx users!
>>
>> I am running a 5ns md simmula
. I have got two cpt files
md_1_0.cpt and md_1_0_prev.cpt. which one is to be used?
Also I did not get a md_1_0.gro file/ Is is due to incomplete simmulation?
Also do I need to specify -append flag or not? I am using version 5.1.5
Please need urgent answer.
Regards
Neelam Wafa
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Gromacs Users
okay got it.
with dt =2fs250 nsteps are for 5 ns simmulation.
On Thu, 12 Apr 2018 10:35 pm Justin Lemkul, <jalem...@vt.edu> wrote:
>
>
> On 4/12/18 1:33 PM, neelam wafa wrote:
> > Thank you sir justin.
> > I am confused a bit. Kindly tell me which on
Thank you sir justin.
I am confused a bit. Kindly tell me which one of the following is right for
5 ns.
nsteps =500; 500=5000 ps (5ns)
or
nsteps = 250 ; 2*250= 5000 ps (5ns).
On Thu, 12 Apr 2018 10:13 pm Justin Lemkul, <jalem...@vt.edu> wrote:
>
>
> On 4/12/18
Dear gmx users,
I have run the md simmulation of my protein ligand complex for 1ns
following the conditions used in tutorial by sir Justin. Now I want to run
the simmulations for 5ns and 10 ns. How have set it like this:
integrator = md; leap-frog integrator
nsteps = 500; 2
Thanks sir Mark and Justin.
I ll try to figure it out with the administer. But in case the problem is
not resolved, is it okay if I run the commands directly through terminal?
Will it effect the results?
I know it ll be a tedious job.
Regards
Neelam Wafa
On Mon, 9 Apr 2018 10:03 pm Justin
-c ../NPT/npt$LAMBDA.gro -p
$FREE_ENERGY/Methane/topol.top -t ../NPT/npt$LAMBDA.cpt -o md$LAMBDA.tpr
mdrun -nt 2 -deffnm md$LAMBDA
echo "Production MD complete."
# End
echo "Ending. Job completed for lambda = $LAMBDA"
On Mon, Apr 9, 2018 at 4:56 PM, neelam wafa <neelam.w
for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
---
job.sh: line 65: mdrun: command not found
similar errors I get for all the sets.
Regards
Neelam Wafa
On Mon, Apr 9, 2018 at 3:30 PM, Justin Lemkul
but not through
the job.sh.
Please suggest me a solution. Sorry for the long text or for addressing
directly to you.
Thanks in advance.
Regards
Neelam wafa
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ok thanks.
On 2 Mar 2018 22:25, "Justin Lemkul" <jalem...@vt.edu> wrote:
>
>
> On 3/2/18 12:18 PM, neelam wafa wrote:
>
>> Thanks Justin
>>
>> Can you please suggest me any article or reading that can help me to
>> understand the f
are
> trying to do except it involves pdb2gmx
>
> Mark
>
> On Fri, Mar 2, 2018, 18:15 neelam wafa <neelam.w...@gmail.com> wrote:
>
> > Is there any way to fix this problem with the start and end terminals?
> >
> > On 2 Mar 2018 22:12, "neelam wafa"
Thanks Justin
Can you please suggest me any article or reading that can help me to
understand the factors to be considered while choosing a force field or to
parameterize the ligand?
On 1 Mar 2018 18:14, "Justin Lemkul" <jalem...@vt.edu> wrote:
>
>
> On 3/1/18 8
Is there any way to fix this problem with the start and end terminals?
On 2 Mar 2018 22:12, "neelam wafa" <neelam.w...@gmail.com> wrote:
> Thanks dear
>
> So it means I can continue with rest of the process. Will it not effect
> the results?
>
> On 1 Mar
Thanks dear
So it means I can continue with rest of the process. Will it not effect the
results?
On 1 Mar 2018 19:53, "Justin Lemkul" <jalem...@vt.edu> wrote:
On 3/1/18 9:35 AM, neelam wafa wrote:
> Hi!
> Dear all I am running pdb2gmx command to create the protein
Hi!
Dear all I am running pdb2gmx command to create the protein topology but
getting this error. please guide me how to fix this problem.
WARNING: WARNING: Residue 1 named TRP of a molecule in the input file was
mapped
to an entry in the topology database, but the atom H used in
an interaction of
Dear gmx users
I am trying to run a protein ligand simmulation. How can i create topolgy
for ligand. prodrg topology is not reliable then which server or software
can be used? can topology be created by T LEEP off ambertools package for
gromacs??
secondly how to select the boxtype as I am new to
thanks. problem resolved.
On 21 Feb 2018 08:13, "Justin Lemkul" <jalem...@vt.edu> wrote:
>
>
> On 2/20/18 9:50 PM, neelam wafa wrote:
>
>> Dear gmx users
>>
>> I am still stuck at this point.
>> error obtained is this
>> Fatal error:
&g
is informative. Check the number of entries in the gro file and
> compare it with the [ atoms ] section in your topology, together with
> anything that's added under [ system ]. The total numbers need to match.
>
> Alex
>
>
>
> On 2/18/2018 11:34 AM, neelam wafa wrote
Dear gmx users,
I am doing the tutorial of protein ligand simmulation given at
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/com.
when I give following command, I get an error.
gmx grompp -f em.mdp -c solv.gro -p topol.top -o ions.tpr
the error says the number of
-- Forwarded message --
From: "neelam wafa" <neelam.w...@gmail.com>
Date: 17 Feb 2018 00:57
Subject: how to get .mdp files
To: <gromacs.org_gmx-users-ow...@maillist.sys.kth.se>
Cc:
Hi
I am new to this list. I have run the gromacs tutorial ' lysosime in
wat
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