[gmx-users] Entering ions

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

Re: [gmx-users] Entering ions

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

Re: [gmx-users] Entering ions

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

[gmx-users] umbrella Sampling and PMF- Error estimation

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

Re: [gmx-users] umbrella Sampling and PMF- Error estimation

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

Fwd: [gmx-users] umbrella Sampling and PMF- Error estimation

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

Re: [gmx-users] pdb files from trajectory

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,

[gmx-users] Published articles which have used Gromcas for their work

/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

Re: [gmx-users] FEP

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

[gmx-users] Gravity force in equation of motion

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

Re: [gmx-users] PMF curve

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

Re: [gmx-users] PMF curve

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

Re: [gmx-users] PMF curve

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

Re: [gmx-users] PMF curve

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

Re: [gmx-users] PMF curve

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

Re: [gmx-users] how to obtain binding energy

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

Re: [gmx-users] Umberella sampling

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

Re: [gmx-users] Umberella sampling

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

[gmx-users] Continuation=yes From?

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

Re: [gmx-users] Continuation=yes 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

Re: [gmx-users] Continuation=yes From?

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

Re: [gmx-users] Docking

A: Discussion list for GROMACS users gmx-users@gromacs.org 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.yes,you are right. Regarding question 2: I have a pdf file from Docking Server for sertraline-SERT

[gmx-users] Articles using Gromacs to do simulation, calculation, evaluation

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

[gmx-users] Docking

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

Re: [gmx-users] Docking

...@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

Re: [gmx-users] rationale behind tcoupling ligand with protein instead of with SOL

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

[gmx-users] Extending Simulation

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

[gmx-users] NPT.mdp parameters NOTE

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

Re: [gmx-users] Extending Simulation

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

Re: [gmx-users] Extending 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

[gmx-users] converging value

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

Re: [gmx-users] converging value

) 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

Re: [gmx-users] How to remove charge of 5e-2 ??

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

Re: [gmx-users] How to remove charge of 5e-2 ??

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

Re: [gmx-users] How to remove charge of 5e-2 ??

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

Re: [gmx-users] How to remove charge of 5e-2 ??

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

Re: [gmx-users] How to remove charge of 5e-2 ??

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

[gmx-users] not enough space

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

[gmx-users] Re: not enough space

) 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

[gmx-users] Umberella sampling

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

Re: [gmx-users] domain decomposition

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

Re: [gmx-users] domain decomposition

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

[gmx-users] domain decomposition

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

Re: [gmx-users] Is there still interest in rigid-body simulation?

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

[gmx-users] g_rms g-rmsd

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

[gmx-users] pick in pull.xvg

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

Re: [gmx-users] g_rms g-rmsd

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

[gmx-users] g_sham

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

[gmx-users] plot of force via time

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

Re: [gmx-users] plot of force via time

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

Re: [gmx-users] Pulling

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

Re: [gmx-users] Pulling

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

Re: [gmx-users] Umberella sampling

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

[gmx-users] Fwd: membrane protein

-- 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

[gmx-users] Fwd: membrane-protein

-- 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

[gmx-users] Grandcanonical Ensemble

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

[gmx-users] Umberella sampling

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

[gmx-users] Pulling

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

Re: [gmx-users] versions

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

Re: [gmx-users] versions

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

[gmx-users] terminated but not completely

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

[gmx-users] versions

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

[gmx-users] membrane protein

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

[gmx-users] parallel running

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

Re: [gmx-users] parallel running

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

Re: [gmx-users] parallel running

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

Re: [gmx-users] parallel running

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

Re: [gmx-users] parallel running

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

Re: [gmx-users] parallel running

...@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

[gmx-users] membrane-protein

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

[gmx-users] membrane-protein tutorial

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

Re: [gmx-users] membrane-protein tutorial

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

Re: [gmx-users] membrane-protein tutorial

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

Re: [gmx-users] membrane-protein tutorial

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

[gmx-users] Membrane-protein tutorial

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

Re: [gmx-users] Active site

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

[gmx-users] Active site

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

Re: [gmx-users] Active site

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

Re: [gmx-users] PRODRG

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

Re: [gmx-users] PRODRG

, 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

[gmx-users] PRODRG

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

[gmx-users] topology with all hydrogens

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

Re: [gmx-users] topology with all hydrogens

, 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

[gmx-users] Charge groups

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

[gmx-users] Re: Charge groups

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

[gmx-users] Charge groups

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

[gmx-users] validation of ligand parametrization

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

Re: [gmx-users] validation of ligand parametrization

? 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

Re: [gmx-users] validation of ligand parametrization

: 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

[gmx-users] Gromos96 manual and user guid

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

Re: [gmx-users] PRODRG server

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

[gmx-users] PRODRG server

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

Re: [gmx-users] PRODRG server

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

Re: [gmx-users] GROMOS96 topology for small molecule

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

[gmx-users] PRODRG server

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 --

Re: [gmx-users] so difficult problem

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

Re: [gmx-users] so difficult problem

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

Re: [gmx-users] so difficult problem

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

Re: [gmx-users] so difficult problem

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

Re: [gmx-users] so difficult problem

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

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