sure, thank you.
On Mon, Oct 21, 2013 at 4:49 PM, Justin Lemkul wrote:
>
>
> On 10/21/13 8:54 AM, Mohsen Ramezanpour wrote:
>
>> Dear Dr. Justin
>>
>> Thank you for your reply
>>
>> You are right, I am sorry for my mistake. I meant Phosphate and Sulfat
Dear Dr. Justin
Thank you for your reply
You are right, I am sorry for my mistake. I meant Phosphate and Sulfate
ions.
I want to have these ions in my solution.
On Mon, Oct 21, 2013 at 1:37 PM, Justin Lemkul wrote:
>
>
> On 10/21/13 4:45 AM, Mohsen Ramezanpour wrote:
>
&
Dear users
I want to use some ions in my simulation (Phosphorus, Sulfur and ...).
How can I know in which FF these are present?
And what can I do if no FF include the interested Ions?
any suggestion is appreciated in advacne
Best
Mohsen
--
gmx-users mailing listgmx-users@gromacs.org
http://
ting of GBFE is 2 kj/mol ?
Thanks in advance
Best
On 7/31/13, Mohsen Ramezanpour wrote:
> Thank you for your reply Dr. Justin
>
> On 7/31/13, Justin Lemkul wrote:
>>
>>
>> On 7/31/13 7:00 AM, Mohsen Ramezanpour wrote:
>>> Hi everyone
>>>
>>>
Thank you for your reply Dr. Justin
On 7/31/13, Justin Lemkul wrote:
>
>
> On 7/31/13 7:00 AM, Mohsen Ramezanpour wrote:
>> Hi everyone
>>
>> How can we have an error estimation for Gibbs binding free energy when
>> I do umbrella sampling and PMF profile?
Hi everyone
How can we have an error estimation for Gibbs binding free energy when
I do umbrella sampling and PMF profile?
Actually I did an umbrella sampling for protein and ligand complex and
I have a PMF profile now but I do not know how much is my error!
Thanks in advance for any suggestion
Dear Shima
What is the name of your .tpr file?
If you had not chosen any name for it, Gromacs will generate a
topol.tpr for you and in my idea this error will not occur,
if not, you have to mention your file (e.g. Filename.tpr) explicitely
in your command line!
I hope this help you
Best
On Sun,
/About_Gromacs/Citations
in the result of my search there are some articles which has not used
gromacs but because of some reasons it has cited Gromacs.
Please let me know how can I have a list of all publications by Gromacs.
Thanks in advance for your guidances
Best
Mohsen Ramezanpour
--
gmx-users
Hi
Please have a look at Dr.Justin tutorial page at the following link:
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/index.html
Cheers
On Mon, Oct 10, 2011 at 12:27 PM, Steven Neumann wrote:
> Hi Gmx Users,
>
> Can you suggest some reading and some tutorial in calculat
Thank you for your reply.
I think so
On Wed, Jun 1, 2011 at 12:01 PM, Jianguo Li wrote:
> Seems gravity is much weaker than the other forces in molecular simulations
> and thus can be neglected.
> Jianguo
>
> --
> *From:* mohsen ramezanpour
>
Dear All
There is a question about applied forces in MD equations of motion.
Where do we insert Gravity in our equation?
In the other words :
Had we ignored gravity force in our equations?
Why?
Actually I read manual but I weren't answered.
Thanks in advance
--
gmx-users mailing listgmx-use
On Mon, May 30, 2011 at 10:10 PM, Justin A. Lemkul wrote:
>
>
> mohsen ramezanpour wrote:
>
>> Dear Dr.Justin
>>
>> There is not any answer?
>>
>>
> Please have a bit of patience. I'm not your personal answer service. You
> just happened t
Dear Dr.Justin
There is not any answer?
On Mon, May 30, 2011 at 7:58 PM, mohsen ramezanpour <
ramezanpour.moh...@gmail.com> wrote:
> Yes,you are right
> I need to do more sampling.But the second attached file was just to
> transfer my mean :)
> My final PMF curve is the f
starting point?
0.18 (with negative value ) OR 0.03 (with about zero value) OR the average
in that region?
Because there is a difference about 0.5 kcal/mol .
Thanks in advance
On Mon, May 30, 2011 at 7:42 PM, Justin A. Lemkul wrote:
>
>
> mohsen ramezanpour wrote:
>
>> Thank you
, Justin A. Lemkul wrote:
>
>
> mohsen ramezanpour wrote:
>
>> Thank you for your reply
>>
>> Actually my system is not the same as tutorial.
>>
>
> Then you should not equate the results, or be concerned when things look
> different. Every system is d
resultedin the whole of my curve.
Is not it strong(wonderfull?)?
On Mon, May 30, 2011 at 6:57 PM, Justin A. Lemkul wrote:
>
>
> mohsen ramezanpour wrote:
>
>> Dear Dr.Justin
>>
>> Regarding to PMF curve which resulted from Umbrella sampling:
>> I obtained the
Dear Dr.Justin
Regarding to PMF curve which resulted from Umbrella sampling:
I obtained the following curve.
Dose it mean?Because it is not similar to yours in tutorial :(
if yes,please let me know what is the Delta G value approximately?
Because I don't know difference between which points is my
Dear Shahab
Yes,when you compute delta Gibbs energy of binding ,You can compute binding
constant(Kd or Ki)
by thermodynamics relations as Dr.Justin said.
I think both methods can be applied to any systems which you wish to have
its binding free energy.
(including protein-protein,protein-ligand ,p
Dear Shahab
You need to do one of the following methods;
1-Umbrella Sampling and computing PMF curve
2-Thermodynamic Integration
Please read some tutorials by Dr.Justin ,
It can be very useful
Be success
On Tue, May 17, 2011 at 3:08 PM, shahab shariati
wrote:
> Dear gromacs users
>
>
> my sim
Thank you very much
I understood completely
Best
On Sun, May 8, 2011 at 7:30 PM, Justin A. Lemkul wrote:
>
>
> mohsen ramezanpour wrote:
>
>> Dear Dr.Justin
>>
>> Thank you for your complete explanation.
>> Please let me discribe where is NPT.cpt comes fro
t the information for npt ensemble.
What do you think
Thanks in advance for your reply
On Sun, May 8, 2011 at 7:03 PM, Justin A. Lemkul wrote:
>
>
> mohsen ramezanpour wrote:
>
>> Dear Dr.Justin
>>
>> I didn't any equilibration for any windows! Because:
>>
if I use NPT.enr OR NPT.trr OR in
grompp(especially NPT.enr) ?
Because all of information about NPT step are included in this files.
Thanks in advance for your
On Sun, May 8, 2011 at 5:47 PM, Justin A. Lemkul wrote:
>
>
> mohsen ramezanpour wrote:
>
>> Dear Dr.Justi
Dear Dr.Justin
Regarding doing umbrella sampling:
I used gen_vel =no
and I prefer to use from thermodynamics of system in NPT.cpt
Although the T and P were as I did set in NPT.mdp file (T=310 ,P=1 bar)
But their values in my umbrela.log files are not as before (for example
P=-8.434578e+1)
Wher
Thank you for your detailed axplain
I understood completely
On Mon, May 2, 2011 at 4:34 PM, Justin A. Lemkul wrote:
>
>
> mohsen ramezanpour wrote:
>
>> Dear Dr.Justin
>>
>> Thank you for your reply
>> My is Protein-ligand,It is have the same conditions as
27 PM, Justin A. Lemkul wrote:
>
>
> mohsen ramezanpour wrote:
>
>> Dear Dr.Justin
>>
>> Regarding Umbrella Sampling tutorial:
>>
>> The CONTINUATION option in md_umbrella.mdp is YES,
>> and you have noticed : From NPT
>>
>> I can't u
Dear Dr.Justin
Regarding Umbrella Sampling tutorial:
The CONTINUATION option in md_umbrella.mdp is YES,
and you have noticed : From NPT
I can't understand it's reason correctly!
we run a NPT and then Pulling, then extracted some configurations from
pull.trr file.
I think we must continue from p
ham * escribió:
>
>
> De: Mark Abraham
> Asunto: Re: [gmx-users] Docking
> A: "Discussion list for GROMACS users"
> Fecha: miércoles, 27 de abril de 2011, 5:27
>
> On 4/27/2011 7:52 PM, mohsen ramezanpour wrote:
>
> Dear Mark
> Thank you for your reply.ye
ote:
> On 4/27/2011 7:05 PM, mohsen ramezanpour wrote:
>
>> Dear Users
>>
>> I read so many emails to mailing list, there were important notes about
>> docking but I couldn't extract a general result.
>> Please let me know:
>>
>> 1-Can we dock a
Dear Users
I read so many emails to mailing list, there were important notes about
docking but I couldn't extract a general result.
Please let me know:
1-Can we dock a ligand to it's protein's binding pocket with Pymol and
Gromacs as following?
first:locating ligand outside and close to binding
Dear All
How can I get a list of all articles which have used Gromacs Package for
their work?
I looked at citations for 4 principal papers in gromacs website,but most of
them were not simulations but
improving algorithms such as lincs and etc.
Some packages as Lammps saves articles which use lam
Hi peter
I think the important is to don't couple small number of atoms(ligand
molecules or a few ions) separately to a reference tempreture!
It probably will result the same if you make two tcouple groups as below:
Protein-LIG water-ions
or
Proteinwater-ions-LIG
I think they will be equvale
file)
Do you have any idea?
I know it is not any problem if a quantity is oscilating around it's
converged value.
thanks in advance for your reply
On Sun, Apr 10, 2011 at 3:09 PM, Mark Abraham wrote:
> On 10/04/2011 6:48 PM, mohsen ramezanpour wrote:
>
>> Dear All
>>
Dear All
How can I determine the converged value of a simulation?
Because the pressure has big oscilations around it's converging value but it
is difficult to determine that value.
can everybody guide me?
Thanks in advance
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.o
Dear Dr.Mark
Thank you very much
you are right
I understood your mean exactly,
On Sun, Apr 10, 2011 at 12:44 PM, Mark Abraham wrote:
> On 10/04/2011 6:04 PM, mohsen ramezanpour wrote:
>
> Dear Dr.Mark
>
> On Sun, Apr 10, 2011 at 12:20 PM, Mark Abraham wrote:
>
>> On 10
Dear Dr.Mark
On Sun, Apr 10, 2011 at 12:20 PM, Mark Abraham wrote:
> On 10/04/2011 5:40 PM, mohsen ramezanpour wrote:
>
>> Dear All
>> I used the following commands accoring to Extending Simulation in
>> gromacs/Documentation/how-tos/Extending Simulation
>> to exte
Dear Dr.Justin
As you have noticed in your tutorials,It is better to use Nose-Hoover for
tempreture in the NPT.mdp file.
You have used tau-t = 0.1 in most of your md.mdp files for generating npt
ensemble.
When I use a npt file with these settings,there is a Note as following:
sorry,i can't rememb
Dear All
I used the following commands accoring to Extending Simulation in
gromacs/Documentation/how-tos/Extending Simulation
to extend my simulation.
I entered:
tpbconv -s npt-1.tpr-extend 100 -o npt-1-extend.tpr
nohup mpirun -np 4 mdrun -s npt-1-extend.tpr -cpi npt-1.cpt
Ii run this
Thank you very much Dr.Justin for your important notes
On Wed, Apr 6, 2011 at 8:09 PM, Justin A. Lemkul wrote:
>
>
> mohsen ramezanpour wrote:
>
>> Dear Dr.Justin
>> I had asked this question before but unfortunately I didn't answered
>> good!
>>
Dear Dr.Justin
I had asked this question before but unfortunately I didn't answered good!
Instead of Pulling and separating some structures in definite distances,
I located my drug in definite distances along z axis (as my initial
structures for doing umbrella sampling).
Am I right?
The main pro
(ns/day) (hour/ns)
Performance:174.935 8.226 0.690 34.784
gcq#92: "Once Again Let Me Do This" (Urban Dance Squad)
what it means?
Why they worked if they were wrong??
On Wed, Apr 6, 2011 at 4:59 PM, mohsen ramezanpour <
ramezanpour.moh...@gmail.com> wrote:
>
Dear All
I used mdrun for generating NVT
It crashed and massage was:
Trying to get md5sum: nvt-1.trr: Stale NFS file handle
Trying to get md5sum: nvt-1.edr: Stale NFS file handle
---
Program mdrun, VERSION 4.5.3-dev-20110310-a52f8-dirty
Source
rotein!
I was wrong,we can't do that
> Erik
>
> mohsen ramezanpour skrev 2011-04-06 09.13:
>
> Daer Dr.Mark
>
> You are right,But all of them(as I know) have integer charges!
> the problem is simullating a system with partial charges.
> We absolutely have such syst
Thank you.
I read it and I understood your mean.
On Wed, Apr 6, 2011 at 11:52 AM, Mark Abraham wrote:
> On 06/04/11, *mohsen ramezanpour * wrote:
>
> Daer Dr.Mark
>
> You are right,But all of them(as I know) have integer charges!
> the problem is simullating a system with par
Daer Dr.Mark
You are right,But all of them(as I know) have integer charges!
the problem is simullating a system with partial charges.
We absolutely have such systems.
On Wed, Apr 6, 2011 at 11:22 AM, Mark Abraham wrote:
> On 6/04/2011 4:45 PM, mohsen ramezanpour wrote:
>
> Dear
Dear Dr.Justin
What can we do (how can neutralize system) if the total charge of our system
was not integer?
I think there is not any solution and we have to simulate a charged system
not a neutral.
Am I right?
Thanks in advance
On Wed, Apr 6, 2011 at 11:12 AM, mohsen ramezanpour
Dear Dr.Justin
I had the same problem.
I modified the charges and charge groupsin the topology of a drug.the net
charge of it is zero(I am sure)
though,when I used pdb2gmx it resulted a NOTE like the following:
NOTE:The system has non-zero total charge: 3.03e00
I continued simulation and ign
le of protein?
Thanks in advance
On Tue, Apr 5, 2011 at 11:58 AM, Mark Abraham wrote:
> On 5/04/2011 5:09 PM, mohsen ramezanpour wrote:
>
>> Dear Mark
>>
>> Actually I don't know why.
>> I just did the normal process as other my simulations.
>>
>> Let me
raham wrote:
> On 4/04/2011 1:51 AM, mohsen ramezanpour wrote:
>
>> Dear All
>>
>> I have a file which contains afew residues (noncontinuous),
>> When I use mdrun on a computer(4 cpu) I am facing with the following
>> Error:
>>
>> Fatal error:
&g
Dear All
I have a file which contains afew residues (noncontinuous),
When I use mdrun on a computer(4 cpu) I am facing with the following Error:
Fatal error:
There is no domain decomposition for 4 nodes that is compatible with the
given box and a minimum cell size of 3.28697 nm
Change the number
Welcome :)
It is absolutely useful.
On Mon, Mar 28, 2011 at 2:32 AM, Adam Herbst wrote:
> Hi all,
> I have seen a few posts on gmx-users indicating a desire to treat certain
> atom groups as rigid bodies in MD simulations. I just started implementing
> this, and so far I have it working for tra
> the list.
>
> Chris.
>
> -- original message --
>
> plot of force via time
> mohsen ramezanpour ramezanpour.mohsen at gmail.com
> Sat Mar 19 14:49:40 CET 2011
>
>* Previous message: [gmx-users] g_sham
>* Messages sorted by: [ date ] [ thread ] [ subject
Dear All
I have a plot,Force via time.(pull.xvg in pulling)
what is important,the value of force in each time or its average? because it
is oscilationg around a line.
I am in doubt , because the important in tempreture and pressure coupling
were thier averages not their values in time.
Thanks in
Dear All
I have a trajectory file for 500 ps simulation
I used g_sham tool,the output was an ener.xvg file (0-40 on y axis and 0-33
on x axis ??!!)
But I don't know what quantities are ploted via eachother?
Please let me know
Thanks in advance
--
gmx-users mailing listgmx-users@gromacs.org
h
m once ;)
>
> Cheers,
>
> Tsjerk
>
> On Mar 19, 2011 12:16 PM, "mohsen ramezanpour" <
> ramezanpour.moh...@gmail.com> wrote:
>
> Dear All
>
>
>
> I have a trajectory(.xtc) and its corresponding .tpr file:
> I used the following commands s
Dear All
I did a pulling simulation for protein-drug system.
My output (pull.xvg) has a pick in 100 ps (equivalent to 1 nm),
the rest of plot is flat(of course with oscilation around the average),of
course with NOT ZERO average in the flat region.
Can I result ?
" the interaction between protein
Dear All
I have a trajectory(.xtc) and its corresponding .tpr file:
I used the following commands separately but the results were
different,Why??
g_rms-f trajectory.xtc-s structure.tpr-n index.ndx-o
rms.xvg
I choosed group number 12 (drug in pulling problem) for two choose
Thank you again for your reply
On Wed, Mar 16, 2011 at 7:35 PM, wrote:
> 2-When you limit your sampling phase space,it can make some Errors,
>> Because you may ignore some important regions(where you don't know them
>> and you can't predict there).
>>
>
> I agree with the idea that underlies you
-- Forwarded message --
From: mohsen ramezanpour
Date: Tue, Mar 8, 2011 at 11:33 PM
Subject: membrane-protein
To: Discussion list for GROMACS users
Dear All
doing membrane protein tutorial of Dr.Justin I have a few question,
1-Why do I need to know the stabilization state of
-- Forwarded message --
From: mohsen ramezanpour
Date: Wed, Mar 9, 2011 at 2:49 PM
Subject: membrane protein
To: Discussion list for GROMACS users
Dear All
in membrane protein tutorial:
What is the P-N vector?
RMSD for what group do I need to calculate?
How can I estimate
Dear chris
Thanks for your reply
1-I am not sure,Since we need the know the variations of free energy along a
specific degree of freedom of system(for example z axis),so the springs
must be 1 dimensional to allow drug to oscilate only in one dimension(z
axis).
Let me say my question in other word
Dear Chris
Thanks for your reply
2-When you limit your sampling phase space,it can make some Errors,Because
you may ignore
some important regions(where you don't know them and you can't predict
there).
In the other hands,When we pull drug along a line,although we had not
restrain it, but in fact t
Dear All
Afew question about Pulling in Umberella Sampling
1-the goal of pulling is making some primary structures (in different
distances) to do umberella sampling for each one of them.
I can make these states by transporting my ligands along a vector to
prepare these primary structures.Is this
Dear All
afew question in umberella sampling tutorial:
1-We do umberella sampling for each of 25 simulation windows,while using a
spring(harmonic potential),Are these springs 1 or 3 dimensional?
2-Suppose the length of one windows is X nm,what is the approperiate K
(spring constant) for this wind
Dear All
1-Does Gromacs support Grandcanonical ensemble too?
2-I want to increase the length of my simulation box during simulation,Is it
possible?
3-As a result.I want to do my simulation in grandcanonical in the following
way:
As the length of my simulation box is increasing,I want to full the
Dear All
I run a simulation for 4 days.
Unfortunately it terminated,but not completely,1 steps from 2 has
done.
Is there any way to run the continue of my files?
Thanks in advance for your guidances
Best Regards
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/
The exact Error is this:
Program g_energy, VERSION 4.0.7
Source code file: ../../../../src/gmxlib/enxio.c, line: 118
Fatal error:
You are trying to read an edr file of GROMACS version 4.1 or later with
GROMACS version 4.0
On Sat, Mar 12, 2011 at 2:46 PM, mohsen ramezanpour <
ramezanpour.
t you to create a new topology
> with the 4.0.7 version.
>
>
> Il 12/03/2011 08:54, mohsen ramezanpour ha scritto:
>
> Dear All
>>
>> How can I read and work on outputs of one version of Gromacs with tools
>> of other version?
>> Because I have run my program o
Dear All
How can I read and work on outputs of one version of Gromacs with tools of
other version?
Because I have run my program on cluster(version 4.5.3) ,but I need to work
with them in v.4.0.7
Suppose I have to work with this version and there is not any way to change
versions neighter on clu
Dear All
in membrane protein tutorial:
What is the P-N vector?
RMSD for what group do I need to calculate?
How can I estimate the helix tilt?
Thanks in advance
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
Dear All
doing membrane protein tutorial of Dr.Justin I have a few question,
1-Why do I need to know the stabilization state of my box vector?
2-How can I do this (with wich program?)?
3-What can I do if they were not stable?
Thanks in advance
Mohsen
--
gmx-users mailing listgmx-users@gro
Dear All
doing membrane protein tutorial of Dr.Justin I have a few question,
Please let me know their answers.
1-Why do I need to use a tempreture upper than lipid phase transition
tempreture for equilibration section?
2-What the lipid phase transition means exactly?
Thanks in advance for you
emkul wrote:
>
>
> mohsen ramezanpour wrote:
>
>
>>
>>
>> On Tue, Mar 8, 2011 at 2:49 PM, Esztermann, Ansgar <
>> ansgar.eszterm...@mpi-bpc.mpg.de <mailto:ansgar.eszterm...@mpi-bpc.mpg.de>>
>> wrote:
>>
>>
>> >> You don
On Tue, Mar 8, 2011 at 2:49 PM, Esztermann, Ansgar <
ansgar.eszterm...@mpi-bpc.mpg.de> wrote:
>
> >> You don't use qsub or bsub?
> >
> > No,What is these?How can I prepare and use them?
>
> They are commands to submit jobs to batch systems.
>
> thank you.Please let me know more if it is possible
T
On Tue, Mar 8, 2011 at 2:53 PM, Esztermann, Ansgar <
ansgar.eszterm...@mpi-bpc.mpg.de> wrote:
>
> On Mar 8, 2011, at 12:00 , mohsen ramezanpour wrote:
> >
> >> > Besides when I used the following command I get an executeable Error:
> >> > mpirun
On Tue, Mar 8, 2011 at 1:40 PM, Esztermann, Ansgar <
ansgar.eszterm...@mpi-bpc.mpg.de> wrote:
>
> On Mar 8, 2011, at 10:26 , mohsen ramezanpour wrote:
>
> > 4- nohup mpirun -np 8 mdrun -deffnm output &
> >
> > The result is running mdrun on
ource to your job.
> Jianguo
> ------
> *From:* mohsen ramezanpour
> *To:* Discussion list for GROMACS users
> *Sent:* Tuesday, 8 March 2011 17:26:19
> *Subject:* [gmx-users] parallel running
>
> Dear All
>
> I want to run gromacs in parallel
Dear All
I want to run gromacs in parallel on cluster.for this I follow below steps:
1-I connect to a node with ssh comand,fro example: ssh compute-o-1
2-cd scratch
3-grompp -f md.mdp-c input.gro-o output.tpr -p
topol.top -n index.ndx
4- nohup mpirun -np 8 mdrun -de
Dear Dr.Justin
Is there any criteria for choosing vdwradii for carbon atoms?
Because I have changed it from 0.15 to 0.375,but there were afew water
molecules,it is difficult to delete them manually.
then I decided to increase the vdwradii to 0.450
it is better now but i think the gap between water
Ok.Thank you very much
On Mon, Mar 7, 2011 at 6:29 PM, Justin A. Lemkul wrote:
>
>
> mohsen ramezanpour wrote:
>
>> Dear Dr.justin
>> Thank you.You are right.
>> I did what you said.
>>
>> please let me know the answer of my other question in first e
iteration.
In the other words it seems it dosen't converge!!
What do you think?
Thanks in advance
On Mon, Mar 7, 2011 at 6:09 PM, Justin A. Lemkul wrote:
>
>
> mohsen ramezanpour wrote:
>
>> Dear Dr.Justin
>> Yes,I know,it deleted some lipids according to inflateGRO scri
for your reply
On Mon, Mar 7, 2011 at 5:42 PM, Justin A. Lemkul wrote:
>
>
> mohsen ramezanpour wrote:
>
>> Dear all
>>
>> I am doing Membrane -protein tutorial.
>> Actually I did each step carefully,I could score down my lipids 26 times.
>> But the
Dear all
I am doing Membrane -protein tutorial.
Actually I did each step carefully,I could score down my lipids 26 times.
But there were two problems:
1-I get ~77 A for area per lipid in 26th step not 71 as Dr.Justin has said
2-I tried to do more iteration to make closer my area per lipid to 71,Bu
me know if there are any other
Thanks in advance for your reply
On Sun, Feb 13, 2011 at 3:55 PM, Justin A. Lemkul wrote:
>
>
> mohsen ramezanpour wrote:
>
>> Dear Dr.Justin
>>
>> I couldn't find any tutorial for doing free energy cycles with gromacs.
>
nt to learn how I can do this.
Thanks in advance for your guidance
On Sat, Feb 12, 2011 at 4:50 PM, Justin A. Lemkul wrote:
>
>
> mohsen ramezanpour wrote:
>
>> Dear All
>>
>> I want to evaluate the binding free energy of protein-dryg.
>>
>> My protein ha
Dear All
I want to evaluate the binding free energy of protein-dryg.
My protein has so many atoms(5000 atoms),it make running too long.
I want to use Umbrella sampling for this.
Can I separate active site of protein (a radious of 3 nm around of my drug
)and do my work on this system?
Thanks in a
tin A. Lemkul wrote:
>
>
> mohsen ramezanpour wrote:
>
>> Dear Dr.Justin
>>
>> I have read this section before.
>> There are 2 problem:
>> 1:ADDHYD atomname and DELHYD atomname commands dosen't work!
>> they result in ERROR in PRODRG
>>
9, 2011 at 9:42 AM jorge_quint...@ciencias.uis.edu.co wrote:
>>
>> > I think that is better to use antechamber tools.
>> >
>> >
>> > > On 10/02/2011 3:40 AM, mohsen ramezanpour wrote:
>> > >> Dear Users
>> > >>
>> > >>
Dear Users
I am using PRODRG to make topology for my drug
It addes Hydrogenes but in wrong way.
My Nitrogen atom is bonded to 2 Carbos,
and PRODRG addes 2 Hydrogenes to it .
Please let me know how can I do.
Thanks in advance
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.
>
> Tsjerk
>
> On Feb 6, 2011 9:42 AM, "mohsen ramezanpour"
> wrote:
>
> Dear All
>
> I want to generate a topology file in 43A1 force field for a small
> molecule.
> Of course I want one which contains all hydrogens in that.
> PRODRG doesn't generate like
Dear All
I want to generate a topology file in 43A1 force field for a small molecule.
Of course I want one which contains all hydrogens in that.
PRODRG doesn't generate like this.do you know another server with these
conditions?
Thanks in advance
Mohsen
--
gmx-users mailing listgmx-users@gro
with this size of charge group,what table extention is enough?
Thanks in advance
On Sun, Feb 6, 2011 at 10:37 AM, mohsen ramezanpour <
ramezanpour.moh...@gmail.com> wrote:
> Dear All
>
> I read charge groups section in the gromacs manual.
> I have a question.please let m
Dear All
I read charge groups section in the gromacs manual.
I have a question.please let me know it's answer.
Is it necessary that our charge groups be made of afew number of atoms?
in the other words ,if I have a charge group with 50 atom,Is my results
valid?
I didn't see anywhere in manual to
Dear All
Suppose I determined partial charges on atoms of my molecules.
How can I make charge groups of them?
For example I have a drug of 50 atom(of course along with it's hidrogenes),
and all of my data for charges are as 1.3465728 (suppose they are accurate
and different to eachother)
Is it p
PM, mohsen ramezanpour wrote:
>
> Dear Justin
> I don't want to rely on PRODRG server as others.
> I want to do my work as accurate as possible.
> Absolutely I read your papar and I know PRODRG present bad results for
> estimating free energies.
> I want to parametrize my drug
this in your papers?
Thanks in advance for your reply
On Wed, Jan 26, 2011 at 3:14 PM, Justin A. Lemkul wrote:
>
>
> mohsen ramezanpour wrote:
>
>> Dear All and specially Dear Dr.Justin
>> I generated parameters for a typical ligand.
>> now I want to validate it.
&g
Dear All and specially Dear Dr.Justin
I generated parameters for a typical ligand.
now I want to validate it.
How can I do it?
Please let me know references for doing this.
Of course I have read the article by Dr.Justin(Alzeimer),Unfortunately I
couldn't understand it completely and very good.
Is t
ks in advance for your help
On Mon, Jan 24, 2011 at 4:01 PM, Justin A. Lemkul wrote:
>
>
> mohsen ramezanpour wrote:
>
>> Dear Dr.justin
>> Actually by doing this we are using two different force fields in one
>> simulation.
>> I had done it before and
rges of my
drug?
for example ABINIT or Gaussian!
Thanks in advance
On Sat, Jan 22, 2011 at 8:03 PM, Justin A. Lemkul wrote:
>
>
> mohsen ramezanpour wrote:
>
>> Ok
>> then,I can use PRODRG server to generate .top and .gro files for drug.
>> since it's r
Dear All
I need GROMOS96 manual and user guid for my work.
Can you send it for me?
Thanks in advance for your help.
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Sear
r our protein with 53A6 too.
and work completely with 53A6.
Am i right?
thanks in advance
On Sat, Jan 22, 2011 at 4:43 PM, Justin A. Lemkul wrote:
>
>
> mohsen ramezanpour wrote:
>
>> Dear Justin
>>
>> I read your articles about PRODRG server,they were very usefu
1 - 100 of 167 matches
Mail list logo
