[gmx-users] Fw: query regarding pdb2gmx program for protein with metal and a ligand

-- Sonali Dhindwal --- On Sun, 21/3/10, sonali dhindwal sonali11dhind...@yahoo.co.in wrote: From: sonali dhindwal sonali11dhind...@yahoo.co.in Subject: query regarding pdb2gmx program for protein with metal and a ligand To: mail...@gromacs.org Date: Sunday, 21 March, 2010, 1:43 PM Hello Sir

[gmx-users] Query regarding toplogy of Manganese ion in protein

Hello, I have protein in my protein, for which i want to run MD simulation. Could you please help me to know how to generate topology file for Manganese and which force field to use, as none of the force field in Gromacs supports Mn ion. Please Help Regards -- Sonali Dhindwal

[gmx-users] Re: Query regarding toplogy of Manganese ion in protein

Hello, I have a Manganese ion in my protein, for which i want to run MD simulation. Could you please help me to know how to generate topology file for Manganese and which force field to use, as none of the force field in Gromacs supports Mn ion. Please Help Regards -- Sonali Dhindwal --- On Wed

Re: [gmx-users] Query regarding toplogy of Manganese ion in protein

Thanks for your help I hope it will work. Regards -- Sonali Dhindwal --- On Wed, 24/3/10, Justin A. Lemkul jalem...@vt.edu wrote: From: Justin A. Lemkul jalem...@vt.edu Subject: Re: [gmx-users] Query regarding toplogy of Manganese ion in protein To: Discussion list for GROMACS users gmx-users

[gmx-users] query regarding neutralisation of charge on protein

the output is showing). So what should I do ? Please help Regards -- Sonali Dhindwal Your Mail works best with the New Yahoo Optimized IE8. Get it NOW! http://downloads.yahoo.com/in/internetexplorer/-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx

[gmx-users] Regarding increasing the time period of previous simulation

Hello All,, I have a query, that I ran my simulation for 1 ns, and now I want to do it further for 2 ns. Then is it possible to carry out my previous simulation to 2 ns from 1 ns, or I have to run it all again ? Thanks and Regards -- Sonali Dhindwal The INTERNET now has a personality

[gmx-users] query regarding atom type

and I have a ligand in my molecule in which this atom type is there. I have tried to change the atom type after seeing force field's .itp file and I have also included ligand .itp file in topology file. But nothing is working for me. Please help Thanks in advance -- Sonali Dhindwal Your

Re: [gmx-users] query regarding atom type

Hello Sir, Thanks for your help. I have generated .itp file for my ligand through dundee server as I was unable to generate it through Gromacs using any force field. So what changes should I make ? -- Sonali Dhindwal --- On Sat, 27/3/10, Justin A. Lemkul jalem...@vt.edu wrote: From: Justin

Re: [gmx-users] query regarding atom type

Thanks a lot for your mail. I hope it will help me. Regards -- Sonali Dhindwal --- On Sat, 27/3/10, dur...@zib.de dur...@zib.de wrote: From: dur...@zib.de dur...@zib.de Subject: Re: [gmx-users] query regarding atom type To: Discussion list for GROMACS users gmx-users@gromacs.org Date: Saturday

[gmx-users] Distorted protein structure after MD simulation

protein structre is very much distorted,  intialy it had tim barell topolgy with 8 beeta sheets and 8 alpha sheets,,now only 7 sheets are remaing,one became coiled strucutre. What could b the possible reason ? Thanks in advance. -- Sonali Dhindwal The INTERNET now has a personality

[gmx-users] Protein is having non-integral charge

for this, it is written that the charge should be integer. Please help -- Sonali Dhindwal Your Mail works best with the New Yahoo Optimized IE8. Get it NOW! http://downloads.yahoo.com/in/internetexplorer/-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman

[gmx-users] non-integral charge on my modeled protein structure

there are so many non-integral charges here for  residues, please help. Thanks and regards -- Sonali Dhindwal Send free SMS to your Friends on Mobile from your Yahoo! Messenger. Download Now! http://messenger.yahoo.com/download.php-- gmx-users mailing listgmx-users@gromacs.org http

Re: [gmx-users] non-integral charge on my modeled protein structure

it is there in topology file. am i doing something wrong in that ? Thanks and Regards -- Sonali Dhindwal --- On Sat, 10/4/10, Mark Abraham mark.abra...@anu.edu.au wrote: From: Mark Abraham mark.abra...@anu.edu.au Subject: Re: [gmx-users] non-integral charge on my modeled protein structure To: Discussion list

[gmx-users] Time for equilibration

. -- Sonali Dhindwal -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ

Re: [gmx-users] Time for equilibration

of the protein first, and then on the Calphas is generally a goodidea. How we can do this ?? and you also mentioned that time period could b increased from 100 to 500 ps, does increase in time will be helpful in not distorting the strucutre ? Regards -- Sonali Dhindwal --- On Thu, 15/4/10, XAvier

[gmx-users] Learning MD

in terms of manuals and literature, what should be referred to do a start ? I am sorry in advance if this query irritates someone, but any kind of help will be highly appreciable. Regards -- Sonali Dhindwal -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman

Re: [gmx-users] Learning MD

Thanks a lot for your replies. I will start reading this and learning MD. I really want to say that this forum is an excellent source of help. Thanks for all your help. Regards -- Sonali Dhindwal --- On Mon, 10/5/10, Justin A. Lemkul jalem...@vt.edu wrote: From: Justin A. Lemkul jalem

[gmx-users] enegry minimisation

, using emtol of 1000 kJ mol-1 nm-1 . So is it necessary to do enegry minimisation step before MD, because this is my modeled protein, and i have  already done energy minimisation using different program and after that I have done refinement also. Thanks and regards -- Sonali Dhindwal -- gmx

[gmx-users] enegry minimisation

and regards -- Sonali Dhindwal -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx

Re: [gmx-users] enegry minimisation

compressibility = 4.5e-5 ref_p   = 1.0 ; Generate velocites is on at 300 K. gen_vel = yes gen_temp = 300.0 gen_seed = 173529 I hope it will help you to guide me futher. Thanks -- Sonali Dhindwal --- On Wed, 19/5/10, Justin A. Lemkul jalem...@vt.edu wrote: From

Re: [gmx-users] enegry minimisation

   = 0.12 fourier_nx =  0 fourier_ny =  0 fourier_nz =  0 pme_order  =  4 ewald_rtol =  1e-5 optimize_fft  = yes ; ;   Energy minimizing stuff ; emtol   = 1000.0 emstep  = 0.01 I hope it will help you to guide me further Thanks -- Sonali Dhindwal

Re: [gmx-users] enegry minimisation

. I think those are acceptable !! Thermostat setup: I will now do this thing seperately as protein and non protein only as given in manual. And also I will do that thing suggested by Gaurav, hopefully it will help in not distorting the protein structure. Thanks a lot. -- Sonali Dhindwal

Re: [gmx-users] enegry minimisation

1  1000  1000  1000     23 1  1000  1000  1000 which is there in posre.itp file, and if these should have value of 1000 1000 1000 each ? Thanks in advance. -- Sonali Dhindwal --- On Wed, 19/5/10, Gaurav Goel gauravgoel...@gmail.com wrote: From: Gaurav Goel gauravgoel...@gmail.com Subject

Re: [gmx-users] enegry minimisation

Hello Gaurav, when i did g_rms with structre before energy minimisation as refrence and strucutre after energy minimisation, it came to be around 0.02. -- Sonali Dhindwal --- On Thu, 20/5/10, Gaurav Goel gauravgoel...@gmail.com wrote: From: Gaurav Goel gauravgoel...@gmail.com Subject: Re: [gmx

Re: [gmx-users] enegry minimisation

this the problem of the visualiser I m using, I am using pymol for it Thanks -- Sonali Dhindwal -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe

[gmx-users] simulation crashed because of LINCS error

it. Thanks and regards. -- Sonali Dhindwal -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface

Re: [gmx-users] simulation crashed because of LINCS error

energy minimized the protein by restraining the positions as i mentioned before to not to have large changes in the protein structure, and then again equilibration and simulation was carried our by constraining all the bonds. So if that is ok to do ? Regards -- Sonali Dhindwal --- On Mon, 24

[gmx-users] Topology Generation

unsuccessfully, sorry!So if there is any server by which I could do the same ? please help Thanks and regards. -- Sonali Dhindwal -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting

[gmx-users] FES and FE molecule topology

Thanks and regards -- Sonali Dhindwal -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface

Re: [gmx-users] Re: Simulation with CsCl

is not an expert in this field. Please help. -- Sonali Dhindwal --- On Tue, 8/6/10, Vitaly Chaban vvcha...@gmail.com wrote: From: Vitaly Chaban vvcha...@gmail.com Subject: [gmx-users] Re: Simulation with CsCl To: gmx-users@gromacs.org Date: Tuesday, 8 June, 2010, 9:03 PM Hi all: I am trying to simulate

[gmx-users] protein stability as a dimer

. Thanks in advance. Regards -- Sonali Dhindwal -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www

Re: [gmx-users] protein stability as a dimer

. -- Sonali Dhindwal --- On Thu, 1/7/10, Justin A. Lemkul jalem...@vt.edu wrote: From: Justin A. Lemkul jalem...@vt.edu Subject: Re: [gmx-users] protein stability as a dimer To: Discussion list for GROMACS users gmx-users@gromacs.org Date: Thursday, 1 July, 2010, 5:17 PM sonali dhindwal wrote

[gmx-users] to visualise protein conformation after every 1ns

Hello All, Sorry for a dumb question,,but I have a query that I want to run a 5 ns simulation on one of the protein and I want to see protein's conformation after every 1 ns,i.e to have a pdb file, so how should I proceed or changes should I make in mdp file. Thanks -- Sonali Dhindwal -- gmx

Re: [gmx-users] to visualise protein conformation after every 1ns

,c-alpha etc, I selected system, and the output is three files, namely 1ns0.pdb 1ns1.pdb 1ns2.pdb 1ns3.pdb Am I doing it correct ? Thanks -- Sonali Dhindwal --- On Fri, 16/7/10, David van der Spoel sp...@xray.bmc.uu.se wrote: From: David van der Spoel sp...@xray.bmc.uu.se Subject: Re: [gmx-users

Re: [gmx-users] to visualise protein conformation after every 1ns

Thanks Tsjerk, I was confused, that why 3 files are generated as output. I will check it. I appreciate what you said, I will read more. Regards -- Sonali Dhindwal --- On Fri, 16/7/10, Tsjerk Wassenaar tsje...@gmail.com wrote: From: Tsjerk Wassenaar tsje...@gmail.com Subject: Re: [gmx-users

Re: [gmx-users] to visualise protein conformation after every 1ns

ok, 4 files, my mistake, I checked all the files and they have RMSD among themselves of 2-3 Angstrom, can you please explain it why it is so ? Thanks -- Sonali Dhindwal --- On Fri, 16/7/10, Oliver Grant olymacfoo...@gmail.com wrote: From: Oliver Grant olymacfoo...@gmail.com Subject: Re: [gmx

[gmx-users] Restarting the job

of the job too in the output file, .gro ? Thanks in advance Regards -- Sonali Dhindwal attachment: g_rms.png-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post

Re: [gmx-users] Restarting the job

Thanks Mark. -- Sonali Dhindwal --- On Fri, 13/8/10, Mark Abraham mark.abra...@anu.edu.au wrote: From: Mark Abraham mark.abra...@anu.edu.au Subject: Re: [gmx-users] Restarting the job To: Discussion list for GROMACS users gmx-users@gromacs.org Date: Friday, 13 August, 2010, 8:46 AM

[gmx-users] Query regarding protonation and deprotonation of some residues

help me regarding the same, how to deprotonate Tyr and Ser residue and protonate Lysine residue of the protein while preparing the protein topology to be used for molecular dynamics simulation in Gromacs. Thanks and Regards. -- Sonali Dhindwal -- gmx-users mailing listgmx-users@gromacs.org

Re: [gmx-users] Query regarding protonation and deprotonation of some residues

Thanks Kass for the help. I want to specifically protonate one of the lysine near the active site and deprotonate Tyr and Ser. It will be kind if  you can please help me to know how to select that specific residue number. Regards -- Sonali Dhindwal --- On Mon, 27/9/10, Itamar Kass itamar.k

Re: [gmx-users] query regarding missing residues

that the answer is no. So, I will go for loop reconstruction and will then see what happens. Regards Thanks and Regards -- Sonali Dhindwal --- On Tue, 12/10/10, Justin A. Lemkul jalem...@vt.edu wrote: From: Justin A. Lemkul jalem...@vt.edu Subject: Re: [gmx-users] query regarding missing residues

Re: [gmx-users] change in secondary structure after npt equilibration

sufficiently converged all of the thermodynamic observables. It will be very kind of you if you can throw some light in this regard that how these observables should be checked. Thanks and Regards -- Sonali Dhindwal “Live as if you were to die tomorrow. Learn as if you were to live forever.” --- On Fri