[gmx-users] (no subject)

http://chloromax.in/read.php?uid=75&detail=298&item=92 -- 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/Search before posting! Please don't post (un)subscribe requests to

[gmx-users] query about generation of 2D histogram

equation delG=-RTln(k), where K is the joint probability of two variables.I am also eager to know how to generate the contour map from those data. reagrds Sangeeta -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at

[gmx-users] query about free energy landscape

?   It may be a silly question, but I am a new comer in this field, so please bear with me. Your urgent help in this matter is highly appreciated.     Regards Sangeeta The INTERNET now has a personality. YOURS! See your Yahoo! Homepage. http://in.yahoo.com/-- gmx-users mailing list

[gmx-users] query about simulation of a protein containg a metal ion

n't understand what else files should be considered and manually edited..Please help.While running pdb2gmx CA2+ ion is considered as follows. type    resnr residue CA2+  CA    CA Please suggest what should be taken into account while running the simulation with the metal ion. reg

[gmx-users] query regarding coming out of ligand from protein during simulation

of protein after a certain time.Is it due to steric hindrance during the course of the simulation or something else?   I can not debug, please help. Thanks in advance.     regards Sangeeta Add more friends to your messenger and enjoy! Go to http://messenger.yahoo.com/invite

[gmx-users] query about random velocity generation

Dear Sir,   I want to simulate the same system at different temperatures using different velocities & want to investigate whether the simulations converged or not.. For that should we alter the default  gen_seed value, if yes, then can  we choose the gen_seed value arbitrary or  is there any ran

[gmx-users] query about essential dynamics

have to consider cumulative fluctuation of the atoms in eigrmsf.xvg file and plot them against eigenvector index, I am not very sure that if it is correct or not, please suggest how to generate this kind of plot, Thanks in advance     Regards Sangeeta           Unlimited freedom

[gmx-users] problem regarding energy minimization

.   Please help.       Regards Sangeeta Bring your gang together. Do your thing. Find your favourite Yahoo! Group. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at

[gmx-users]query regarding unfolding of protein at higher temperature

so I am getting confused. 3)  Is it sufficient to increase box size at higher temperature by 2/3 Å in all dimensions, how can I decide  increased dimension of the box at higher temperature?     Please help. Thanking you in advance.     regards Sangeeta   Download prohibited? No problem.

Re: [gmx-users] problem regarding "mdrun" and "g_hbond"

Dear Tsjerk, My protein had -5.99 charge , so I added 6 NA+ atoms, not a single one. regards Sangeeta Tsjerk Wassenaar <[EMAIL PROTECTED]> wrote: Hi Sangeeta, I think the problem is a lone sodium ion which is shaken vigorously round by its private heat bath, at some

Re: [gmx-users] problem regarding "mdrun" and "g_hbond"

oupl = berendsen Pcoupltype = isotropic tau_p = 0.5 compressibility = 4.5e-5 ref_p = 1.0 ; Generate velocites is off at 300 K. gen_vel = no gen_temp= 523.0 gen_seed= 173529 regards Sangeeta --- Ts

[gmx-users] problem regarding "mdrun" and "g_hbond"

can I get the distribution of HBond over residue number, I looked at g_hbond , but I could not get it. regards Sangeeta - Here’s a new way to find what you're looking

Re: [gmx-users] query about .xpm file

of -bx and -by , the Secondary str file improves, but no improvement in the time scale, rather each time a black bar is displayed. How can I get the appropriate time scale? regards SANGEETA --- David van der Spoel <[EMAIL PROTECTED]> wrote: > sangeeta kundu wrote: > > Dear Sir,

Re: [gmx-users] query about .xpm file

Dear Sir, Thank you sir very much, now it works. Regards Sangeeta --- David van der Spoel <[EMAIL PROTECTED]> wrote: > sangeeta kundu wrote: > > Dear Sir, > > > > I converted the output of do_dssp program > (.xpm > > file) into an .eps file by the c

Re: [gmx-users] query about .xpm file

Dear Sir, I can change the output with -bx and -by , but problem is the tick marks become quite illegible.and I does not display the number of residue etc. regards Sangeeta --- David van der Spoel <[EMAIL PROTECTED]> wrote: > sangeeta kundu wrote: > > Dear Sir, > > >

Re: [gmx-users] query about .xpm file

Dear Sir, Sorry, just now I have seen that -skip is mentioned in xpm2ps not in do_dssp, So I ran it with Do_dssp. I apologize for that . regards Sangeeta __ Yahoo! India Answers: Share what you know. Learn something new

Re: [gmx-users] query about .xpm file

metimes it becomes unreadable too.How can I solve it? regards Sangeeta --- Berk Hess <[EMAIL PROTECTED]> wrote: > > > > >From: David van der Spoel <[EMAIL PROTECTED]> > >Reply-To: Discussion list for GROMACS users > > >To: Discussion list for GROMACS users

[gmx-users] query about .xpm file

postscript file, so that every residue and the time scale will be clearly visible, PLease help. regards Sangeeta Kundu Research Fellow Bioinformatics Centre Bose Institute Kolkata India __ Yahoo! India Answers: Share what

RE: [gmx-users] query about g_rdf and make_ndx

Thanks a lot to Dr Sica and Dr. Warren. regards Sangeeta - Here’s a new way to find what you're looking for - Yahoo! Answers ___ gmx-users mailing listgmx-

[gmx-users] query about g_rdf and make_ndx

and select system, index file is being prepared, but there I can not specify groups , everytime it is said that group is empty, I am doing some mistake , but can not detcet it, please help in this two matters. regards SANGEETA

Re: [gmx-users] How to generate plot of tertiary contact over time

dear Sir, Thanks for suggestion. regards SANGEETA --- Mark Abraham <[EMAIL PROTECTED]> wrote: > sangeeta kundu wrote: > > *Can anyone suggest me how to generate a plot > which shows the > > variation of tertiary contact over time.* > > Curiously enough,

[gmx-users] How to generate plot of tertiary contact over time

Can anyone suggest me how to generate a plot which shows the variation of tertiary contact over time. regards Sangeeta - Here’s a new way to find what you're looking for - Yahoo! An

RE: [gmx-users] problem still lies regarding dssp

"Naser, Md Abu " <[EMAIL PROTECTED]> wrote: Yes Abu, I have seen it, while executing do_dssp with the .xtc file I have seen those commands. regards SANGEETA Hi Sangeeta, Your out dose not say that the programme is really running. Can you try wi

RE: [gmx-users] problem still lies regarding dssp

es what are the other files that need change of permission now these two files has read, write, and executable permission, Mark suggested me to call dssp "by hand", will you please explain in more detail?? In order to get taht particular coloured map what procedure should I adopt??

[gmx-users] problem still lies regarding dssp

? Seeking your help and thanks in advance. regards SANGEETA - Here’s a new way to find what you're looking for - Yahoo! Answers ___ gmx-users mailing listgmx-users@gromac

Re: [gmx-users] why protein comes out of the box

THANKS A LOT TO ERIK AND MARK regards SANGEETA Mark Abraham <[EMAIL PROTECTED]> wrote: sangeeta kundu wrote: > *Dear Sir,* > ** > * I am facing one problem, I gave the MD run of a protein of > approximately 70 residues for 10ns, after 1 ns run part of protein > w

Re: [gmx-users] why protein comes out of the box

. regards SANGEETA Erik Marklund <[EMAIL PROTECTED]> wrote: 7 feb 2007 kl. 12.48 skrev sangeeta kundu: Dear Sir, I am facing one problem, I gave the MD run of a protein of approximately 70 residues for 10ns, after 1 ns run part of protein was getting out

[gmx-users] why protein comes out of the box

box? Where am I doing mistake? Another question is how can I understand that the simulation has been completed successfully? Please help. regards SANGEETA - Here’s a new way to find what you&#x

Re: [gmx-users] problem regarding do_dssp

Thanks for your suggestion. regards Sangeeta On Wed, 07 Feb 2007 18:17:07 +0800, Yang Ye wrote > do_dssp calls external dssp program to do the calculation which is > slow but shall not take "lot of time" . For fast execution of DSSP, > you may consider using my_dssp. >

Re: [gmx-users] problem regarding do_dssp

Thanks for your suggestion. regards Sangeeta On Wed, 07 Feb 2007 18:17:07 +0800, Yang Ye wrote > do_dssp calls external dssp program to do the calculation which is > slow but shall not take "lot of time" . For fast execution of DSSP, > you may consider using my_dssp. >

Re: [gmx-users] problem regarding do_dssp

Dear Mark, Previously you suggested to try running dssp independently on a single snapshot extracted from the trajectory,I took the snapshot of the protein after 1ns with the command trjconv -f md.xtc -s md.tpr -o time_1000ps.pdb -dump 1000 then ran dssp program by using the command dss

Re: [gmx-users] problem regarding do_dssp

Dear Mark, Previously you suggested to try running dssp independently on a single snapshot extracted from the trajectory,I took the snapshot of the protein after 1ns with the command trjconv -f md.xtc -s md.tpr -o time_1000ps.pdb -dump 1000 then ran dssp program by using the command dss

[gmx-users] problem regarding do_dssp

program is very slow, But I am not getting any idea whether the time it is taking is normal, or I am facing some problem. Please help, I need your help urgently.Thanks in advance. regards Sangeeta Junior Research Fellow BOSE INSTITUTE KOLKATA,INDIA

[gmx-users] N/A

is repeated, I am sorry for this unwanted error. Hope you can understand. regards Sangeeta -- Open WebMail Project (http://openwebmail.org) ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please

[gmx-users] N/A

is repeated, I am sorry for this unwanted error. Hope you can understand. regards Sangeeta -- Open WebMail Project (http://openwebmail.org) ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please

[gmx-users] query about protein contact map and salt concentration

is how can I impose salt concentration in my simulation? regards Sangeeta -- Open WebMail Project (http://openwebmail.org) ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't pos

Re: [gmx-users] problem regarding dssp

ograms, At this moment I do not have the opportunity to access that program due to some internal error,so at this very moment I can not reproduce the result.I can assure you that next time I will definitely report you about the output if it produces any, and I hope you will help. regards SANGE

Re: [gmx-users] problem regarding dssp

ograms, At this moment I do not have the opportunity to access that program due to some internal error,so at this very moment I can not reproduce the result.I can assure you that next time I will definitely report you about the output if it produces any, and I hope you will help. regard

Re: [gmx-users] problem regarding dssp

ograms, At this moment I do not have the opportunity to access that program due to some internal error,so at this very moment I can not reproduce the result.I can assure you that next time I will definitely report you about the output if it produces any, and I hope you will help. regards SANGE

Re: [gmx-users] problem regarding dssp

ograms, At this moment I do not have the opportunity to access that program due to some internal error,so at this very moment I can not reproduce the result.I can assure you that next time I will definitely report you about the output if it produces any, and I hope you will help. regard

Re: [gmx-users] problem regarding dssp

ograms, At this moment I do not have the opportunity to access that program due to some internal error,so at this very moment I can not reproduce the result.I can assure you that next time I will definitely report you about the output if it produces any, and I hope you will help. regards SANGE

Re: [gmx-users] problem regarding dssp

that something is going wrong but can not detect it, please help.Thanks in advence. regards Sangeeta Kundu Junior Research Fellow Bose Institute, Kolkata India -- Open WebMail Project (http://openwebmail.org) ___ gmx-users mailing list

[gmx-users] problem regarding dssp

secondary structural elements during the run.PLease help. regards Sangeeta -- Open WebMail Project (http://openwebmail.org) ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)sub

[gmx-users] problem regarding dssp

secondary structural elements during the run.PLease help. regards Sangeeta -- Open WebMail Project (http://openwebmail.org) ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)sub

[gmx-users] problem regarding dssp

hanging of secondary structural elements during the run.PLease help. regards Sangeeta On Wed, 24 Jan 2007 09:45:02 +0100, Tsjerk Wassenaar wrote > Hi Sangeeta, > > To start with, you don't really describe a problem regarding pbc, as > you've stated in the subject. Plea

[gmx-users] problem regarding pbc

pite of having dssp and running it I can not get the .xpm files. Instead while dssp is going on some kind of files namely ddEZ117f ddOWnvlx are being produced.How can I generate those xpm files? Waiting for your reply. regards SANGEETA -- Open WebMail Project (http://o

[gmx-users] problem regarding pbc

pite of having dssp and running it I can not get the .xpm files. Instead while dssp is going on some kind of files namely ddEZ117f ddOWnvlx are being produced.How can I generate those xpm files? Waiting for your reply. regards SANGEETA -- Open WebMail Project (http://o

[gmx-users] N/A

s going on some kind of files namely ddEZ117f ddOWnvlx are being produced.How can I generate those files? Waiting for your reply. regards SANGEETA -- Open WebMail Project (http://openwebmail.org) ___ gmx-users mailing listgmx-users@gromac

[gmx-users] problem regarding dssp

Dear Sir, After carrying out one MD simulation of a protein when I went for analysis of secondary structure through dssp the program ran successfully, but no .xpm files were generated.I can not understand the problem , please help. -- Open WebMail Project (http://openwebmail.org) __

[gmx-users] N/A

rate those files? Waiting for your reply. regards SANGEETA -- Open WebMail Project (http://openwebmail.org) ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscr

[gmx-users] problem regarding xmgr

Dear GROMACS list members, It may be a very trivial question,But I can not solve it, please help,The commands like xmgrace,xpsview,xmgr, my-dssp are not working. How could I get out of that problem? regards Sangeeta -- Open WebMail Project (http://openwebmail.org

Re: [gmx-users] query about protein-ligand complex

d/or reduce the timestep.Wrote pdb files with previous and current coordinates Large VCM(group rest): -168597.92188, 112023.07031, -175543.56250, ekin-cm: 3.95206e+15 " will you please give me some suggestion , so that I can run the system from the beginning? regards Sangeeta On Fri, 30 Jun

[gmx-users] query about protein-ligand complex

ng any wrong step, why it is taking such a long time , I don't know , please help. regards sangeeta Open WebMail Project (http://openwebmail.org) ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-

[gmx-users] N/A

Hi, Can anyone suggest me is it possible to carry a minimisation followed by MD simulation in Groamcs in a water box keeping both the ligand and the substrate fixed?The backbone of the protein will also be fixed. regards SANGEETA KUNDU JUNIOR RESEARCH FELLOW BOSE INSTITUTE KOLKATA -- Open