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
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 jalem...@vt.edu wrote:
On 10/21/13 4:45 AM, Mohsen Ramezanpour wrote:
Dear
sure, thank you.
On Mon, Oct 21, 2013 at 4:49 PM, Justin Lemkul jalem...@vt.edu 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 Sulfate
ions.
I want to have these ions
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
Thank you for your reply Dr. Justin
On 7/31/13, Justin Lemkul jalem...@vt.edu 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?
Actually I did an umbrella
of GBFE is 2 kj/mol ?
Thanks in advance
Best
On 7/31/13, Mohsen Ramezanpour ramezanpour.moh...@gmail.com wrote:
Thank you for your reply Dr. Justin
On 7/31/13, Justin Lemkul jalem...@vt.edu wrote:
On 7/31/13 7:00 AM, Mohsen Ramezanpour wrote:
Hi everyone
How can we have an error
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 s.neuman...@gmail.comwrote:
Hi Gmx Users,
Can you suggest some reading and some
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 list
On Mon, May 30, 2011 at 10:10 PM, Justin A. Lemkul jalem...@vt.edu 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 to catch me at a good time this morning and I was able
the whole of my curve.
Is not it strong(wonderfull?)?
On Mon, May 30, 2011 at 6:57 PM, Justin A. Lemkul jalem...@vt.edu wrote:
mohsen ramezanpour wrote:
Dear Dr.Justin
Regarding to PMF curve which resulted from Umbrella sampling:
I obtained the following curve.
Dose it mean?Because
A. Lemkul jalem...@vt.edu 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 different.
I tried to obtain protein-drug delta G.
I
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 jalem...@vt.edu wrote:
mohsen ramezanpour wrote:
Thank you.
no,I
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 first attached file.
Sorry
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
shahab.shari...@gmail.comwrote:
Dear
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 jalem...@vt.edu wrote:
mohsen ramezanpour wrote:
Dear Dr.Justin
Regarding doing
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 jalem...@vt.edu wrote:
mohsen ramezanpour wrote:
Dear Dr.Justin
I didn't any equilibration for any windows! Because:
As I know the thermodynamics of the system had
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
, Justin A. Lemkul jalem...@vt.edu 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 understand it's reason correctly!
This is a meaningless comment
Thank you for your detailed axplain
I understood completely
On Mon, May 2, 2011 at 4:34 PM, Justin A. Lemkul jalem...@vt.edu wrote:
mohsen ramezanpour wrote:
Dear Dr.Justin
Thank you for your reply
My is Protein-ligand,It is have the same conditions as tutorial.I did
pull ligand
A: Discussion list for GROMACS users gmx-users@gromacs.org
Fecha: miƩrcoles, 27 de abril de 2011, 5:27
On 4/27/2011 7:52 PM, mohsen ramezanpour wrote:
Dear Mark
Thank you for your reply.yes,you are right.
Regarding question 2:
I have a pdf file from Docking Server for sertraline-SERT
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
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
...@anu.edu.auwrote:
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 ligand to it's protein's binding pocket with Pymol and
Gromacs
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
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
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
Dear Dr.Mark
On Sun, Apr 10, 2011 at 12:20 PM, Mark Abraham mark.abra...@anu.edu.auwrote:
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 extend my simulation
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 mark.abra...@anu.edu.auwrote:
On 10/04/2011 6:04 PM, mohsen ramezanpour wrote:
Dear Dr.Mark
On Sun, Apr 10, 2011 at 12:20 PM, Mark Abraham mark.abra
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
)
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 mark.abra...@anu.edu.auwrote:
On 10/04/2011 6:48 PM, mohsen ramezanpour wrote:
Dear All
How can I
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
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
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 mark.abra...@anu.edu.auwrote:
On 6/04/2011 4:45 PM, mohsen ramezanpour wrote
Thank you.
I read it and I understood your mean.
On Wed, Apr 6, 2011 at 11:52 AM, Mark Abraham mark.abra...@anu.edu.auwrote:
On 06/04/11, *mohsen ramezanpour * ramezanpour.moh...@gmail.com wrote:
Daer Dr.Mark
You are right,But all of them(as I know) have integer charges!
the problem
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 systems.
On Wed, Apr 6, 2011 at 11:22 AM, Mark Abraham
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
)
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
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
mark.abra...@anu.edu.auwrote:
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:
There is no domain decomposition for 4 nodes
of protein?
Thanks in advance
On Tue, Apr 5, 2011 at 11:58 AM, Mark Abraham mark.abra...@anu.edu.auwrote:
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 discribe my work in details:
I had
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 ad...@cornell.edu 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
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
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
read them 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 separately but the results were
different,Why??
g_rms-f
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
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
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 ] [ author ]
Dear All
I have a plot,Force via time
Thank you again for your reply
On Wed, Mar 16, 2011 at 7:35 PM, chris.ne...@utoronto.ca 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
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
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
-- Forwarded message --
From: mohsen ramezanpour ramezanpour.moh...@gmail.com
Date: Wed, Mar 9, 2011 at 2:49 PM
Subject: membrane protein
To: Discussion list for GROMACS users gmx-users@gromacs.org
Dear All
in membrane protein tutorial:
What is the P-N vector?
RMSD for what
-- Forwarded message --
From: mohsen ramezanpour ramezanpour.moh...@gmail.com
Date: Tue, Mar 8, 2011 at 11:33 PM
Subject: membrane-protein
To: Discussion list for GROMACS users gmx-users@gromacs.org
Dear All
doing membrane protein tutorial of Dr.Justin I have a few question,
1
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
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
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
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 on cluster(version 4.5.3) ,but I need to
work with them in v.4.0.7
Suppose I have to work
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.moh
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
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
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
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
to your job.
Jianguo
--
*From:* mohsen ramezanpour ramezanpour.moh...@gmail.com
*To:* Discussion list for GROMACS users gmx-users@gromacs.org
*Sent:* Tuesday, 8 March 2011 17:26:19
*Subject:* [gmx-users] parallel running
Dear All
I want to run gromacs in parallel
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 one node(compute-0-1) (on its 4 CPUs)
That's just
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 -np 8 mdrun_mpi -deffnm output
What
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
Thanks in
...@vt.edu 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't use qsub or bsub?
No,What is these?How can I prepare and use them
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 list
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
for your reply
On Mon, Mar 7, 2011 at 5:42 PM, Justin A. Lemkul jalem...@vt.edu 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 there were two problems:
1-I get ~77 A for area
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 jalem...@vt.edu wrote:
mohsen ramezanpour wrote:
Dear Dr.Justin
Yes,I know,it deleted some lipids according to inflateGRO script in the
first
Ok.Thank you very much
On Mon, Mar 7, 2011 at 6:29 PM, Justin A. Lemkul jalem...@vt.edu 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 email:
I am doing iteration more than 26
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
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 jalem...@vt.edu wrote:
mohsen ramezanpour wrote:
Dear Dr.Justin
I couldn't find any tutorial for doing free energy cycles with gromacs.
Then I was forced to select Umbrella
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
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 jalem...@vt.edu wrote:
mohsen ramezanpour wrote:
Dear All
I want to evaluate the binding free energy of protein-dryg.
My protein has so many atoms(5000 atoms),it make running
A. Lemkul jalem...@vt.edu 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
You have to run PRODRG twice. The first time, you get the wrong
, mohsen ramezanpour wrote:
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
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
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 list
, mohsen ramezanpour ramezanpour.moh...@gmail.com
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 this.do you know another server with these
conditions?
Thanks
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
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 me know it's answer
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
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
?
Thanks in advance for your reply
On Wed, Jan 26, 2011 at 3:14 PM, Justin A. Lemkul jalem...@vt.edu wrote:
mohsen ramezanpour wrote:
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
:
On 26/01/2011 11:10 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 drugs
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
drug?
for example ABINIT or Gaussian!
Thanks in advance
On Sat, Jan 22, 2011 at 8:03 PM, Justin A. Lemkul jalem...@vt.edu wrote:
mohsen ramezanpour wrote:
Ok
then,I can use PRODRG server to generate .top and .gro files for drug.
since it's reported charges are not very accurate ,we can
Dear Justin
I read your articles about PRODRG server,they were very useful.
But I have a question:
are charges of functional groups and generally other atom groups the same in
all force fields?
Because you have modified charges of your molecules by Gromos96 53A6 while
prodrg server is generating
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 jalem...@vt.edu wrote:
mohsen ramezanpour wrote:
Dear Justin
I read your articles about PRODRG server,they were very useful.
But I have a question
It is on now,you can use it.
as Justin said you should validate it.
best
On Tue, Jan 18, 2011 at 9:37 PM, Justin A. Lemkul jalem...@vt.edu wrote:
C.Y. Chang wrote:
Hi,
I need to obtain the GROMOS96 topology files (and including the
corresponding PDB files) for some small molecules.
I
Dear All
I generated toplogy file for a drug by PRODG server.
How can I validate it?
i looked at these links but there are not a way for doing that.
http://www.gromacs.org/Documentation/How-tos/Parameterization
http://www.gromacs.org/Downloads/Related_Software/PRODRG#Tips
thanks in advance
--
wrote:
mohsen ramezanpour wrote:
I checked this one but it did not solve the problem.
Actually I did in your way and I found the force is very high on one atom
of my ligand,C12.
I checked it's structure with pymol,it 's situation was normal.
can I change it's coordinate a few?
I think
Sory.
My ligand is Citalopram(a drug)
On Mon, Jan 17, 2011 at 1:35 PM, mohsen ramezanpour
ramezanpour.moh...@gmail.com wrote:
Dear justin
I generated it by PRODRG server,and modifying Protein.top as it is in
ENZYME/DRUG tutorial.
Actually I don't know where is problem.
Ok,I will modify my
how can i do
thanks in advance
On Wed, Jan 12, 2011 at 3:22 PM, mohsen ramezanpour
ramezanpour.moh...@gmail.com wrote:
On Wed, Jan 12, 2011 at 2:59 PM, Mark Abraham mark.abra...@anu.edu.auwrote:
On 12/01/2011 9:37 PM, mohsen ramezanpour wrote:
Dear Dr,Tsjerk
I want to estimate protein
genconf -nbox 2 2 2
Cheers,
Tsjerk
On Jan 6, 2011 7:22 PM, mohsen ramezanpour ramezanpour.moh...@gmail.com
wrote:
Dear Amit
I entered these commands for rotating box:
editconf -f conf.gro -o output.pdb -rotate 0 0 25.4
and then:
editconf -f output.pdb -o newbox.pdb -rotate
that bring you up to this point, and not only the output of
mdrun. That way we can probably see where you go astray.
Cheers,
Tsjerk
On Wed, Jan 12, 2011 at 10:55 AM, mohsen ramezanpour
ramezanpour.moh...@gmail.com wrote:
Dear Dr.Tsjerk
Before doing md for generating NPT, I did an EM
1 - 100 of 155 matches
Mail list logo