Re: [gmx-users] change in secondary structure after npt equilibration
Hi Justin, I am writing in this correspondence, because I also had the same query once that secondary structure changes after equilibration, and you are right that visualisation programs are not always reliable. You also mentioned this time that we should check wether 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, 28/1/11, Justin A. Lemkul wrote: From: Justin A. Lemkul Subject: Re: [gmx-users] change in secondary structure after npt equilibration To: "Discussion list for GROMACS users" Date: Friday, 28 January, 2011, 5:53 PM bharat gupta wrote: > Hi, > > > I am doing a simulation of a 230 amino acid protein for 3ns ... and I have > completed the npt equilibration step .. After retrieving the structure from > npt step and viewing it in pymol, reveals that some portion of the beta > strand got changed to a loop but when I visualized the same structure in VMD > I found that nothing has happened to the structure .. In order to confirm > more ... I generated the SS profile using dssp and I found that , the dssp > shows E i.e. sheet for that region .. So what shall i do next ... shall I > continue with the production step or not ?? > Visualization programs are not always reliable in what they show you, we've discussed that. Methods like DSSP and STRIDE are far more trustworthy, and seem to indicate that your structure is fine. What you should be much more concerned with at this point is whether or not your equilibration sufficiently converged all of the thermodynamic observables. -Justin > -- Bharat > Ph.D. Candidate > Room No. : 7202A, 2nd Floor > Biomolecular Engineering Laboratory > Division of Chemical Engineering and Polymer Science > Pusan National University > Busan -609735 > South Korea > Lab phone no. - +82-51-510-3680, +82-51-583-8343 > > Mobile no. - 010-5818-3680 > E-mail : monu46...@yahoo.com <mailto:monu46...@yahoo.com> > -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing list gmx-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 the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- 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 the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] query regarding missing residues
Hello Justin and Mark, Thanks for the reply. Reason that I didnt apply loop modelling was, for that region it is not given in literature that, this region which consist of 10 residues will form a helix of will remain in loop in an disorganized way. Therefore, I was reluctant in doing loop reconstruction without prior information of this building as loop or helix. And u rightly said that fusing non-corresponding residues will give wrong results, that's why I was asking that if there is way to go for simulation while having some missing residues. But your replies suggest 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 wrote: From: Justin A. Lemkul Subject: Re: [gmx-users] query regarding missing residues To: "Discussion list for GROMACS users" Date: Tuesday, 12 October, 2010, 9:43 PM sonali dhindwal wrote: > Hello Sir, > > I want to ask a question about missing residues, for which coordinates are > not defined in the PDB file. > I have this protein structure and in one of the loop there are some residues > whose coordinates are not defined in the file. > When I did pdb2gmx for preparing the topology, it joined the end of this loop > and renumber ed the whole chain there after. > I searched on net and it was written that missing residues should be modelled > somehow before running simulation, but in my case i cant model this loop > having missing residues because these are very flexible and i cant define > their coordinates through modeling, "Can't" or "haven't tried"? Loop reconstruction, though not trivial, is routinely applied in such cases. That's one of the reasons why programs like Loopy, Modeller, SwissPDBViewer, etc exist. > So, if there is someway through which these residues remain missing and still > I can go ahead with simulation ? You're fusing non-consecutive residues. I would suspect that doing so would have negative implications for your results. -Justin > Thanks in advance. > Regards > > -- > Sonali Dhindwal > > -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing list gmx-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 the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- 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 the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] query regarding missing residues
Hello Sir, I want to ask a question about missing residues, for which coordinates are not defined in the PDB file. I have this protein structure and in one of the loop there are some residues whose coordinates are not defined in the file. When I did pdb2gmx for preparing the topology, it joined the end of this loop and renumber ed the whole chain there after. I searched on net and it was written that missing residues should be modelled somehow before running simulation, but in my case i cant model this loop having missing residues because these are very flexible and i cant define their coordinates through modeling, So, if there is someway through which these residues remain missing and still I can go ahead with simulation ? 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/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
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 wrote:
From: Itamar Kass
Subject: Re: [gmx-users] Query regarding protonation and deprotonation of some
residues
To: "Discussion list for GROMACS users"
Date: Monday, 27 September, 2010, 10:07 AM
Hi,
You need to define the protonation sate vie pdb2gmx.
pdb2gmx -tyr -lys
On 27/09/10 2:34 PM, sonali dhindwal wrote:
Hello All,
I came through this research article, in which author has
selectively deprotonated and protonated some of the
residues to
simulate the condition for electrostatic interaction with
the substrate while carrying out molecular dynamics
simulation.
It will be appreciable, if
you could 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
--
"In theory, there is no difference between theory and practice. But, in
practice, there is." - Jan L.A. van de Snepscheut
===
| Itamar Kass, Ph.D.
| Postdoctoral Research Fellow
|
| Department of Biochemistry and Molecular Biology
| Building 77 Clayton Campus
| Wellington Road
| Monash University,
| Victoria 3800
| Australia
|
| Tel: +61 3 9902 9376
| Fax: +61 3 9902 9500
| E-mail: itamar.k...@monash.edu
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[gmx-users] Query regarding protonation and deprotonation of some residues
Hello All, I came through this research article, in which author has selectively deprotonated and protonated some of the residues to simulate the condition for electrostatic interaction with the substrate while carrying out molecular dynamics simulation. It will be appreciable, if you could 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 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 the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Restarting the job
Thanks Mark. -- Sonali Dhindwal --- On Fri, 13/8/10, Mark Abraham wrote: From: Mark Abraham Subject: Re: [gmx-users] Restarting the job To: "Discussion list for GROMACS users" Date: Friday, 13 August, 2010, 8:46 AM - Original Message ----- From: sonali dhindwal Date: Friday, August 13, 2010 0:59 Subject: [gmx-users] Restarting the job To: Discussion list for GROMACS users > Hello All, > > I have a query regarding the restarts of the jobs after crash. > I want to simulate a protein for 2 ns but in between due to system shutdown, > it stopped, and I made a restart using this command: > mdrun -s topol.tpr -cpi state.cpt -appendnow I checked the rmsd of in between > by producing a .xtc file of the job which ran till now and then checked g_rms > of the simulation, it is showing a graph like this,(I have attached in the > mail) See http://www.gromacs.org/Documentation/How-tos/Graphing_Data for a couple of gnuplot tips. I suspect the weirdness is gnuplot interpreting something as data that it should not interpret as data, and that the contents of the .xvg are actually the second half of normal RMS variation. > this is showing rmsd after the point the job was restarted with some error > in the beginning. > I want to know if there will be error at the end of the job too in the output > file, .gro ? The final .gro will have the final coordinates, as normal. Mark -Inline Attachment Follows- -- gmx-users mailing list gmx-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...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- 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...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Restarting the job
Hello All, I have a query regarding the restarts of the jobs after crash. I want to simulate a protein for 2 ns but in between due to system shutdown, it stopped, and I made a restart using this command: mdrun -s topol.tpr -cpi state.cpt -appendnow I checked the rmsd of in between by producing a .xtc file of the job which ran till now and then checked g_rms of the simulation, it is showing a graph like this,(I have attached in the mail) this is showing rmsd after the point the job was restarted with some error in the beginning. I want to know if there will be error at the end of the job too in the output file, .gro ? 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 interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
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 wrote: From: Oliver Grant Subject: Re: [gmx-users] to visualise protein conformation after every 1ns To: "Discussion list for GROMACS users" Date: Friday, 16 July, 2010, 3:36 PM 0ns, 1ns, 2ns and 3ns gives four files. On 16 July 2010 10:47, sonali dhindwal wrote: 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 wrote: From: Tsjerk Wassenaar Subject: Re: [gmx-users] to visualise protein conformation after every 1ns To: "Discussion list for GROMACS users" Date: Friday, 16 July, 2010, 1:43 PM Sonali, Why wouldn't it be correct if you did just what David told you to do? And how would you be able to check yourself whether you were correct? We can't hold your hand here for every step you make. Have you already gone through the tutorial material linked on the Gromacs website? If not, please do so. In any case, try to feel more confident about yourself. You made it to academia already, didn't you? Cheers, On Fri, Jul 16, 2010 at 9:58 AM, sonali dhindwal wrote: Hello Sir, Thanks for the reply, I tried to run this commad on a simuation which I started to ran for 10 ns,and has already completed around 3 ns I gave trjconv -o 1ns.pdb -dt 1000 -s topol.tpr -f traj.xtc -sep after this it asked for selecting which one I want among, System, protein,bacakbone,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 wrote: From: David van der Spoel Subject: Re: [gmx-users] to visualise protein conformation after every 1ns To: "Discussion list for GROMACS users" Date: Friday, 16 July, 2010, 12:34 PM On 7/16/10 9:02 AM, sonali dhindwal wrote: > 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 > > trjconv -o koko.pdb -dt 1000 -s -f -sep -- David. David van der Spoel, PhD, Professor of Biology Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone:46 18 471 4205fax: 46 18 511 755 sp...@xray.bmc.uu.sesp...@gromacs.org http://folding.bmc.uu.se -- 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...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- 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...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group Groningen Institute for Biomolecular Research and Biotechnology University of Groningen The Netherlands -Inline Attachment Follows- -- 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...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- 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...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -Inline Attachment Follows- -- gmx-users mailing list gmx-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 po
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 wrote: From: Tsjerk Wassenaar Subject: Re: [gmx-users] to visualise protein conformation after every 1ns To: "Discussion list for GROMACS users" Date: Friday, 16 July, 2010, 1:43 PM Sonali, Why wouldn't it be correct if you did just what David told you to do? And how would you be able to check yourself whether you were correct? We can't hold your hand here for every step you make. Have you already gone through the tutorial material linked on the Gromacs website? If not, please do so. In any case, try to feel more confident about yourself. You made it to academia already, didn't you? Cheers, On Fri, Jul 16, 2010 at 9:58 AM, sonali dhindwal wrote: Hello Sir, Thanks for the reply, I tried to run this commad on a simuation which I started to ran for 10 ns,and has already completed around 3 ns I gave trjconv -o 1ns.pdb -dt 1000 -s topol.tpr -f traj.xtc -sep after this it asked for selecting which one I want among, System, protein,bacakbone,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 wrote: From: David van der Spoel Subject: Re: [gmx-users] to visualise protein conformation after every 1ns To: "Discussion list for GROMACS users" Date: Friday, 16 July, 2010, 12:34 PM On 7/16/10 9:02 AM, sonali dhindwal wrote: > 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 > > trjconv -o koko.pdb -dt 1000 -s -f -sep -- David. David van der Spoel, PhD, Professor of Biology Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone:46 18 471 4205fax: 46 18 511 755 sp...@xray.bmc.uu.sesp...@gromacs.org http://folding.bmc.uu.se -- 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...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- 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...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group Groningen Institute for Biomolecular Research and Biotechnology University of Groningen The Netherlands -Inline Attachment Follows- -- gmx-users mailing list gmx-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...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- 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...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] to visualise protein conformation after every 1ns
Hello Sir, Thanks for the reply, I tried to run this commad on a simuation which I started to ran for 10 ns,and has already completed around 3 ns I gave trjconv -o 1ns.pdb -dt 1000 -s topol.tpr -f traj.xtc -sep after this it asked for selecting which one I want among, System, protein,bacakbone,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 wrote: From: David van der Spoel Subject: Re: [gmx-users] to visualise protein conformation after every 1ns To: "Discussion list for GROMACS users" Date: Friday, 16 July, 2010, 12:34 PM On 7/16/10 9:02 AM, sonali dhindwal wrote: > 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 > > trjconv -o koko.pdb -dt 1000 -s -f -sep -- David. David van der Spoel, PhD, Professor of Biology Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 sp...@xray.bmc.uu.se sp...@gromacs.org http://folding.bmc.uu.se -- gmx-users mailing list gmx-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...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- 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...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[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-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...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] protein stability as a dimer
Hi Justin, Sorry for the mistake, I wrote 0.1 ns in "still there are more fluctuations but and it decreses again to 0.28 nm at 0.1 ns." it is 1 ns instead, I ran the simulation for 1ns. I have put the job to run for 1 more ns, so may be there I could analyse something as u said. Thanks a lot. -- Sonali Dhindwal --- On Thu, 1/7/10, Justin A. Lemkul wrote: From: Justin A. Lemkul Subject: Re: [gmx-users] protein stability as a dimer To: "Discussion list for GROMACS users" Date: Thursday, 1 July, 2010, 5:17 PM sonali dhindwal wrote: > Hello All, > I have done simulation for 1ns on a protein dimer using GROMOS96 43a1 force > field. > I want to study if the protein is stable as a dimer or not, so can you > please give me some suggestion as to what analysis I could do for the same. > I checked g_rms after the simulation, graph which I am getting is like, first > rmsd is increases rapidly to 0.2nm for for 0.1 ns and > then till 0.8 ns it still increased to 0.3 nm and > still there are more fluctuations but and it decreses again to 0.28 nm at 0.1 > ns. > > So what could i infer about the stability of the protein as a dimer from this > data. If you've only done 100 ps of simulation, not much. I would also question why you consider it a "decrease" from 0.3 nm to 0.28 nm rather than just a fluctuation. Run a longer simulation to gather meaningful RMSD values. As for other analysis to do, do some homework in the literature, and also consider your own goals for running the simulation. Certainly you have a purpose. -Justin > Thanks in advance. > Regards > > -- > Sonali Dhindwal > > -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing list gmx-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...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- 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...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] protein stability as a dimer
Hello All, I have done simulation for 1ns on a protein dimer using GROMOS96 43a1 force field. I want to study if the protein is stable as a dimer or not, so can you please give me some suggestion as to what analysis I could do for the same. I checked g_rms after the simulation, graph which I am getting is like, first rmsd is increases rapidly to 0.2nm for for 0.1 ns and then till 0.8 ns it still increased to 0.3 nm and still there are more fluctuations but and it decreses again to 0.28 nm at 0.1 ns. So what could i infer about the stability of the protein as a dimer from this data. 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 interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Re: Simulation with CsCl
Hello All , I am also trying to simulate my protein with Mn ion present in it. So can I create the topology entry for Mn ion similar to MG2+ ion ? and how can I get the values of C6 and C12 leonard jones potential in [atom type] entry and will it be required to add [nonbond_params] also ? how can I get them ? Also I want to use Fe2+ also, but it is also not included in gromos force field. This problem of adding other ions and molecule in the system always remains. And being new to this field, can someone suggest in simple terms how to include these considering the person is not an expert in this field. Please help. -- Sonali Dhindwal --- On Tue, 8/6/10, Vitaly Chaban wrote: From: Vitaly Chaban 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 a polysaccharide in solution of water and CsCl, but > cesium is not parametrized in the gromacs 4. I am using the force > field GROMOS 96. > I have looked for the parameters of Cs+ in the OPLS Force field and I have > created 4 files: Cs.atp, Cs.itp, Csnb.itp and Cs.rtp. Also I have include > the parameters for Cs+ in the "ions.itp" file, but it didn't work, Can > someone help me? > Thanks in advance. > Cecilia. Cecilia - You do not need so many files so cesium. Just copy your parameters to the force field used and create the topology entry for cesium similar to [ moleculetype ] Ar 1 [ atoms ] 1 Ar 1 Ar Ar 0 0.0 Do not forget, cesium+ is an ion... -- Dr. Vitaly Chaban -- gmx-users mailing list gmx-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...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- 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...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] FES and FE molecule topology
Hello All, Could some one please help me in introducing Fe2+ and FES molecule in protein for simulation studies. But before starting it, I am not able to generate topology file for the same. I have tried to use HICUP database and used CNS topology file. but it is still not working. 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! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Topology Generation
Hello All, I have to do simulation on one of the protein which contains one dioxy group, as gromacs do not have information to generate toplogy for it, I tried it with PRODRG, but is giving error: ERRDRG> PRODRG does not deal with mono/di-atomic molecules. PRODRG> Program terminated 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! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] simulation crashed because of LINCS error
Thanks Mark for the reply, I think I have mistakenly written 30 instead of 300 for ref_t in temp coupling, So if that could be the problem ? because I have equilbrated the protein before simulation but time is for 20 ps. Is that very short time period? Acually I want to stress here that i have 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, 24/5/10, Mark Abraham wrote: From: Mark Abraham Subject: Re: [gmx-users] simulation crashed because of LINCS error To: "Discussion list for GROMACS users" Date: Monday, 24 May, 2010, 1:00 PM - Original Message ----- From: sonali dhindwal Date: Monday, May 24, 2010 14:32 Subject: [gmx-users] simulation crashed because of LINCS error To: Discussion list for GROMACS users --- | > Hello All, > > With regard to my previous post > http://www.mail-archive.com/gmx-users@gromacs.org/msg30557.html > I have done postion restrained energy minimisation using POSRES.itp file > obtained from pdb2gmx. so that there should not be any large change in the > strucutre of the protein. Note that there are further general recommendations about system preparation here http://www.gromacs.org/Documentation/How-tos/Steps_to_Perform_a_Simulation, i.e. consider not going immediately to your target ensemble. Also, your temperature-coupling is broken in your second .mdp file. Mark > And after that I did equilbration using following mdp file > > title = protein > cpp = /usr/bin/cpp > define = -DPOSRES > constraints = all-bonds > integrator = md > dt = 0.002 ; ps ! > nsteps = 1 ; total 20.0 ps. > nstcomm = 1 > nstxout = 250 ; collect data every 0.5 ps > nstvout = 1000 > nstfout = 0 > nstlog = 10 > nstenergy = 10 > nstlist = 5 > ns_type = grid > rlist = 0.9 > coulombtype = PME > rcoulomb = 0.9 > rvdw = 1.4 > fourierspacing = 0.12 > fourier_nx = 0 > fourier_ny = 0 > fourier_nz = 0 > pme_order = 4 > ewald_rtol = 1e-5 > optimize_fft = yes > ; Berendsen temperature coupling is on in two groups > Tcoupl = V-rescale > tc-grps = Protein Non-Protein > tau_t = 0.1 0.1 > ref_t = 300 300 > ; Pressure coupling is on > Pcoupl = berendsen > tau_p = 0.5 > 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 > > After this, I put the molecule for simulation using the following .mdp file > > title = protein > cpp = /usr/bin/cpp > constraints = all-bonds > integrator = md > dt = 0.002 ; ps ! > nsteps = 50 ; total 1000 ps, 1 ns. > nstcomm = 1 > nstxout = 500 ; collect data every 1 ps > nstvout = 0 > nstfout = 0 > nstlist = 5 > ns_type = grid > rlist = 0.9 > coulombtype = PME > rcoulomb = 0.9 > rvdw = 1.4 > fourierspacing = 0.12 > fourier_nx = 0 > fourier_ny = 0 > fourier_nz = 0 > pme_order = 4 > ewald_rtol = 1e-5 > optimize_fft = yes > ; Berendsen temperature coupling is on in two groups > Tcoupl = V-rescale > tc-grps = Protein Non-Protein > tau_t = 0.1 0.1 > ref_t = 300 30 > ; Pressure coupling is on > Pcoupl = berendsen > tau_p = 0.5 > 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 > > but simulation has crashed showing the error too many Too many LINCS warnings > (1000) > I checked previous posts, it is given that it may be due to incomplete equilibration or putting so many constraints. > So can you please help me in correcting it. > Thanks and regards. > > -- > Sonali Dhindwal | --- > > -- > gmx-users mailing
[gmx-users] simulation crashed because of LINCS error
Hello All, With regard to my previous post http://www.mail-archive.com/gmx-users@gromacs.org/msg30557.html I have done postion restrained energy minimisation using POSRES.itp file obtained from pdb2gmx. so that there should not be any large change in the strucutre of the protein. And after that I did equilbration using following mdp file title = protein cpp = /usr/bin/cpp define = -DPOSRES constraints = all-bonds integrator = md dt = 0.002 ; ps ! nsteps = 1 ; total 20.0 ps. nstcomm = 1 nstxout = 250 ; collect data every 0.5 ps nstvout = 1000 nstfout = 0 nstlog = 10 nstenergy = 10 nstlist = 5 ns_type = grid rlist = 0.9 coulombtype = PME rcoulomb = 0.9 rvdw = 1.4 fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 4 ewald_rtol = 1e-5 optimize_fft = yes ; Berendsen temperature coupling is on in two groups Tcoupl = V-rescale tc-grps = Protein Non-Protein tau_t = 0.1 0.1 ref_t = 300 300 ; Pressure coupling is on Pcoupl = berendsen tau_p = 0.5 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 After this, I put the molecule for simulation using the following .mdp file title = protein cpp = /usr/bin/cpp constraints = all-bonds integrator = md dt = 0.002 ; ps ! nsteps = 50 ; total 1000 ps, 1 ns. nstcomm = 1 nstxout = 500 ; collect data every 1 ps nstvout = 0 nstfout = 0 nstlist = 5 ns_type = grid rlist = 0.9 coulombtype = PME rcoulomb = 0.9 rvdw = 1.4 fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 4 ewald_rtol = 1e-5 optimize_fft = yes ; Berendsen temperature coupling is on in two groups Tcoupl = V-rescale tc-grps = Protein Non-Protein tau_t = 0.1 0.1 ref_t = 300 30 ; Pressure coupling is on Pcoupl = berendsen tau_p = 0.5 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 but simulation has crashed showing the error too many Too many LINCS warnings (1000) I checked previous posts, it is given that it may be due to incomplete equilibration or putting so many constraints. So can you please help me in correcting 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 or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] enegry minimisation
hello Jusitn, Thanks for your reply,, I am sending you the link, so that you can see the changes in the protein, I have specifically shown that part of the protein, where I am seeing changes, http://picasaweb.google.co.in/sonali11dhindwal/Protein?feat=directlink Yello beeta sheets are of the protein after EM, and magenta are that of the refrence structure, you can see how this time,I am surprised myself that sheets have become longer than the refrence structure. I have corrected that define = -DPOSRES also. and have taken that posres file generated by pdb2gmx.is 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 requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
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 wrote: From: Gaurav Goel Subject: Re: [gmx-users] enegry minimisation To: jalem...@vt.edu, "Discussion list for GROMACS users" Date: Thursday, 20 May, 2010, 5:36 PM Can you try using g_rms to compare the difference between the structures before and after EM. -Gaurav On Thu, May 20, 2010 at 7:53 AM, Justin A. Lemkul wrote: > > > sonali dhindwal wrote: >> >> Hello Gaurav, >> Thanks for your reply, >> I did position restrained enegry minimisation, and used following .mdp >> file for the same >> >> title= protein >> cpp = /usr/bin/cpp ; the c pre-processor >> define = -DPOSRE >> constraints = none >> integrator = steep >> dt = 0.002; ps ! >> nsteps = 1000 >> nstlist = 10 >> ns_type = grid >> rlist= 0.9 >> coulombtype = PME >> rcoulomb = 0.9 >> rvdw = 0.9 >> fourierspacing = 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 >> pbc= xyz >> >> I included define = -DPOSRE, for restraining the atom postion, >> I used posre.itp which was genertaed by pdb2gmx. >> >> Have I done it correctly, because after this also many of the beeta sheets >> have become short, forming loops. > > Well, you haven't properly defined position restraints. The default > (produced by pdb2gmx) requires "define = -DPOSRES" not "-DPOSRE." If you > have for some reason modified the topology, then maybe your approach is > correct, but otherwise your position restraints are not being applied. > > I also find it very curious that such substantial changes are taking place > during a simple energy minimization. Are you sure the effects you are > seeing are not simply due to the visualization software you are using > guessing the incorrect secondary structure type? I have had that experience > numerous times, especially in the case of beta-strands. DSSP tells me that, > geometrically, I have beta-strands, but the visualization software renders > coil structures. > > In any case, large structural deviations during EM suggest something > fundamentally wrong with the model. Usually the changes in EM are small, > since it is performed at 0 K. Only huge forces would cause any sort of > structural change. > >> I also want to ask what is the meaning of fx fy and fz : >> > > Force constants (kJ mol^-1 nm^-2) in the x, y, and z directions. > >> ; atom type fx fy fz >> 1 1 1000 1000 1000 >> 5 1 1000 1000 1000 >> 6 1 1000 1000 1000 >> 7 1 1000 1000 1000 >> 8 1 1000 1000 1000 >> 9 1 1000 1000 1000 >>11 1 1000 1000 1000 >>12 1 1000 1000 1000 >>15 1 1000 1000 1000 >>18 1 1000 1000 1000 >>19 1 1000 1000 1000 >>20 1 1000 1000 1000 >>21 1 1000 1000 1000 >>22 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 ? >> > > These default values are typically quite sufficient to restrain the > structure. > > -Justin > >> Thanks in advance. >> -- >> Sonali Dhindwal >> >> >> --- On *Wed, 19/5/10, Gaurav Goel //* wrote: >> >> >>From: Gaurav Goel >>Subject: Re: [gmx-users] enegry minimisation >>To: "sonali dhindwal" >>Date: Wednesday, 19 May, 2010, 8:39 PM >> >>For position restraints you need to do the following: >> >>1. define a name.itp file which looks like: >> >>; In this topology include file, you will find position restraint >>; entries for all the heavy atoms in your original pdb file. >>; This means that all the protons which were added by pdb2gmx are >>; not restrained. >> >>[ position_restraints ] >>; atom type fx fy fz >>1 1 1000 1000 1000 >>5 1 1000 1000 1000 >>6 1 1000 1000 1000 >>... >
Re: [gmx-users] enegry minimisation
Hello Gaurav, Thanks for your reply, I did position restrained enegry minimisation, and used following .mdp file for the same title = protein cpp = /usr/bin/cpp ; the c pre-processor define = -DPOSRE constraints = none integrator = steep dt = 0.002 ; ps ! nsteps = 1000 nstlist = 10 ns_type = grid rlist = 0.9 coulombtype = PME rcoulomb = 0.9 rvdw = 0.9 fourierspacing = 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 pbc = xyz I included define = -DPOSRE, for restraining the atom postion, I used posre.itp which was genertaed by pdb2gmx. Have I done it correctly, because after this also many of the beeta sheets have become short, forming loops. I also want to ask what is the meaning of fx fy and fz : ; atom type fx fy fz 1 1 1000 1000 1000 5 1 1000 1000 1000 6 1 1000 1000 1000 7 1 1000 1000 1000 8 1 1000 1000 1000 9 1 1000 1000 1000 11 1 1000 1000 1000 12 1 1000 1000 1000 15 1 1000 1000 1000 18 1 1000 1000 1000 19 1 1000 1000 1000 20 1 1000 1000 1000 21 1 1000 1000 1000 22 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 wrote: From: Gaurav Goel Subject: Re: [gmx-users] enegry minimisation To: "sonali dhindwal" Date: Wednesday, 19 May, 2010, 8:39 PM For position restraints you need to do the following: 1. define a name.itp file which looks like: ; In this topology include file, you will find position restraint ; entries for all the heavy atoms in your original pdb file. ; This means that all the protons which were added by pdb2gmx are ; not restrained. [ position_restraints ] ; atom type fx fy fz 1 1 1000 1000 1000 5 1 1000 1000 1000 6 1 1000 1000 1000 ... ... _ 1,5,6 etc. are the atom indices you want to restrain. section 4.3.1 in manual. 2. Add "define = -Dname" to your mdp file 3. Add following lines to your topology file ; Include Position restraint file #ifdef name #include "name.itp" #endif 4. compile and run. I'm sure you will find mroe information on position-restrain simulation on gmx-users archive. -Gaurav On Wed, May 19, 2010 at 10:26 AM, sonali dhindwal wrote: Hello Gaurav, Can you please help me in suggesting where should I look for providing parameters to constrain the protein backbone and then do EM and then how to run a short MD simulation by constraining the protein backbone. Sorry to bother you, but as I am new to Gromacs, your help will be highly appreciable. Thanks in advance -- Sonali Dhindwal --- On Wed, 19/5/10, Gaurav Goel wrote: From: Gaurav Goel Subject: Re: [gmx-users] enegry minimisation To: "Discussion list for GROMACS users" Date: Wednesday, 19 May, 2010, 6:44 PM After adding water you can do energy minimization (EM) in two steps: 1. Constrain the protein backbone and do EM. 2. Now do EM on the full system. 3. Run a short MD simulation by constraining the protein backbone. The above three steps will help hydrate the protein molecule with minimal distortion of protein structure. 4. Now run a MD on full system. for details looks here: http://www.google.com/url?sa=t&source=web&ct=res&cd=2&ved=0CBcQFjAB&url=http%3A%2F%2Feugen.leitl.org%2Fchem%2Fkerrigje%2Fpdf_files%2Ffwspidr_tutor.pdf&ei=jOPzS8a3Lab2MdX1_aAO&usg=AFQjCNGB_3mXSQRHuqehBSHXsRyXP1Gymg&sig2=bY3NqXHmruR7eSLVyAuCHQ -Gaurav On Wed, May 19, 2010 at 8:18 AM, sonali dhindwal wrote: Sorry, but I couldnt get your question, I have used this .mdp file for energy minimisation after addition of water and using GROMOS96 43a1 force field : title= drg_trp cpp = /lib/cpp ; location of cpp on SGI define = -DFLEX_SPC ; Use Ferguson’s Flexible water model [4] constraints = none integrator = steep dt = 0.002; ps ! nsteps = 2000 nstlist = 10 ns_type = grid rlist= 0.9 coulombtype = PME ; Use particle-mesh ewald rcoulomb = 0.9 rvdw = 1.0 fourierspacing = 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
Re: [gmx-users] enegry minimisation
Thanks Justin for your help I checked the mdout.mpd, all the parameters were interpereted correctly, though from next time i will take care of putting space. regarding you asked if those are small molecules, yes those are the ligands and i have taken .itp and .gro file from Dundee Prodrg server. 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 --- On Wed, 19/5/10, Justin A. Lemkul wrote: From: Justin A. Lemkul Subject: Re: [gmx-users] enegry minimisation To: "Gromacs Users' List" Date: Wednesday, 19 May, 2010, 5:45 PM sonali dhindwal wrote: > Thanks Justin for your reply. > Yes I have included solvent in the protein using genbox. Then you should do energy minimization after constructing the system. > I am pasting .mdp file which I used for MD simulation : > > title = trp_drg MD > cpp = /lib/cpp ; location of cpp on SGI > constraints = all-bonds > integrator = md > dt = 0.002 ; ps ! > nsteps = 50 ; total 1 ns. > nstcomm =1 I don't know if this matters or not, but I think your parameters and values should be separated from the '=' by whitespace. I also don't know if that will have any effect on your unstable system (see below), but do check to make sure that all of your settings have been interpreted correctly. Confirm your input settings with the mdout.mdp file produced by grompp. > nstxout = 500 ; output coordinates every 1.0 ps > nstvout =0 > nstfout =0 > nstlist = 5 > ns_type = grid > rlist = 0.9 > coulombtype = PME > rcoulomb = 0.9 > rvdw = 1.4 > fourierspacing = 0.12 > fourier_nx =0 > fourier_ny =0 > fourier_nz =0 > pme_order =6 > ewald_rtol = 1e-5 > optimize_fft = yes > ; Berendsen temperature coupling is on in four groups > Tcoupl = berendsen > tau_t = 0.1 0.1 0.1 0.1 0.1 0.1 > tc_grps = Protein SOL MG PEP E4P NA+ > ref_t = 300 300 300 300 300 300 This thermostat setup is certainly incorrect. You should not couple all the components of your system to separate thermostats. See here: http://www.gromacs.org/Documentation/Terminology/Thermostats You have a fairly complicated system. Are some of these species small molecules? If so, how did you derive their parameters? Have you demonstrated that these parameters are accurate? Which structure is falling apart, and how are you making that assessment? -Justin > ; Pressure coupling is on > Pcoupl = berendsen > pcoupltype = isotropic > tau_p = 0.5 > 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 //* wrote: > > > From: Justin A. Lemkul > Subject: Re: [gmx-users] enegry minimisation > To: "Discussion list for GROMACS users" > Date: Wednesday, 19 May, 2010, 5:17 PM > > > > sonali dhindwal wrote: > > Hello All > > This question may sound trivial to many, but as i am new to this > field, please help. > > I want to ask a question regarding my previous query of > distortion of protein strucutre after molecular dynamcs simulation. > > Can you provide a link to your previous post, for reference? > > > I have noticed that after enegry minimisation using steepest > decent algorithm, 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. > > Have you added solvent or anything else to the protein model? If > so, then the answer is yes. Solvation with a regularly-ordered > lattice of solvent molecules can (and often does) lead to bad > clashes with your protein structure, thus necessitating further > minimization. > > There are plenty of reasons why a protein structure might be > unstable, most of them related to .mdp file settings, but you > haven&#
Re: [gmx-users] enegry minimisation
Sorry, but I couldnt get your question, I have used this .mdp file for energy minimisation after addition of water and using GROMOS96 43a1 force field : title = drg_trp cpp = /lib/cpp ; location of cpp on SGI define = -DFLEX_SPC ; Use Ferguson’s Flexible water model [4] constraints = none integrator = steep dt = 0.002 ; ps ! nsteps = 2000 nstlist = 10 ns_type = grid rlist = 0.9 coulombtype = PME ; Use particle-mesh ewald rcoulomb = 0.9 rvdw = 1.0 fourierspacing = 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 --- On Wed, 19/5/10, Erik Marklund wrote: From: Erik Marklund Subject: Re: [gmx-users] enegry minimisation To: "Discussion list for GROMACS users" Date: Wednesday, 19 May, 2010, 5:31 PM sonali dhindwal skrev: > Hello All > This question may sound trivial to many, but as i am new to this field, > please help. > I want to ask a question regarding my previous query of distortion of protein > strucutre after molecular dynamcs simulation. > I have noticed that after enegry minimisation using steepest decent > algorithm, using emtol of 1000 kJ mol^-1 nm^-1 , large amount of distortion > occurs. > 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 > > So how has your system setup changed since your previous EM? Addition of water? Cutoffs? PME? -- --- Erik Marklund, PhD student Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: +46 18 471 4537 fax: +46 18 511 755 er...@xray.bmc.uu.se http://folding.bmc.uu.se/ -- gmx-users mailing list gmx-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...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- 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...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] enegry minimisation
Thanks Justin for your reply. Yes I have included solvent in the protein using genbox. I am pasting .mdp file which I used for MD simulation : title = trp_drg MD cpp = /lib/cpp ; location of cpp on SGI constraints = all-bonds integrator = md dt = 0.002 ; ps ! nsteps = 50 ; total 1 ns. nstcomm =1 nstxout = 500 ; output coordinates every 1.0 ps nstvout =0 nstfout =0 nstlist = 5 ns_type = grid rlist = 0.9 coulombtype = PME rcoulomb = 0.9 rvdw = 1.4 fourierspacing = 0.12 fourier_nx =0 fourier_ny =0 fourier_nz =0 pme_order =6 ewald_rtol = 1e-5 optimize_fft = yes ; Berendsen temperature coupling is on in four groups Tcoupl = berendsen tau_t = 0.1 0.1 0.1 0.1 0.1 0.1 tc_grps = Protein SOL MG PEP E4P NA+ ref_t = 300 300 300 300 300 300 ; Pressure coupling is on Pcoupl = berendsen pcoupltype = isotropic tau_p = 0.5 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 wrote: From: Justin A. Lemkul Subject: Re: [gmx-users] enegry minimisation To: "Discussion list for GROMACS users" Date: Wednesday, 19 May, 2010, 5:17 PM sonali dhindwal wrote: > Hello All > This question may sound trivial to many, but as i am new to this field, > please help. > I want to ask a question regarding my previous query of distortion of protein > strucutre after molecular dynamcs simulation. Can you provide a link to your previous post, for reference? > I have noticed that after enegry minimisation using steepest decent > algorithm, 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. Have you added solvent or anything else to the protein model? If so, then the answer is yes. Solvation with a regularly-ordered lattice of solvent molecules can (and often does) lead to bad clashes with your protein structure, thus necessitating further minimization. There are plenty of reasons why a protein structure might be unstable, most of them related to .mdp file settings, but you haven't posted those so there's no way to know if you're doing things correctly. -Justin > Thanks and regards > ^ > > -- > Sonali Dhindwal > > -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing list gmx-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...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- 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...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] enegry minimisation
Hello All This question may sound trivial to many, but as i am new to this field, please help. I want to ask a question regarding my previous query of distortion of protein strucutre after molecular dynamcs simulation. I have noticed that after enegry minimisation using steepest decent algorithm, using emtol of 1000 kJ mol-1 nm-1 , large amount of distortion occurs. 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-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...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] enegry minimisation
Hello All This question may sound trivial to many, but as i am new to this field, please help. I want to ask a question regarding my previous query of distortion of protein strucutre after molecular dynamcs simulation. I have noticed that after enegry minimisation using steepest decent algorithm, 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-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...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
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 wrote: From: Justin A. Lemkul Subject: Re: [gmx-users] Learning MD To: "Discussion list for GROMACS users" Date: Monday, 10 May, 2010, 10:43 PM sonali dhindwal wrote: > Hello All, > > I am new at MD, and i have started doing it few months ago only. I tried to > run some simulations but taking all the parameters using some tutorials given > online and have not got very good results. > Can someone please help in suggesting what is the best way to learn MD using > Gromacs 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. The Gromacs manual is a fantastic resource, particularly the introductory chapters. Beyond that, have you tried Google? There are a number of great introductory-type pages that discuss some of the more basic aspects of MD. You might also find some help here: http://en.wikipedia.org/wiki/Molecular_dynamics#References I can attest to several of the books listed there (Allen & Tildesley, Leach, and Schlick) being particularly useful. Beyond that, hopefully a supervisor or colleagues will have some expertise and can recommend the requisite reading material. -Justin > Regards > -- > Sonali Dhindwal > > -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing list gmx-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...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- 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...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Learning MD
Hello All, I am new at MD, and i have started doing it few months ago only. I tried to run some simulations but taking all the parameters using some tutorials given online and have not got very good results. Can someone please help in suggesting what is the best way to learn MD using Gromacs 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/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...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Time for equilibration
Thanks for the answer, My protein strucutre is a homology model,,on which i want to do the simulation. and the change in conformation after MD simulation is more than RMSD of 2 Angstrom, that too in the active site of the protein and you said that "Using position restrain on the heavy atoms 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 Periole wrote: From: XAvier Periole Subject: Re: [gmx-users] Time for equilibration To: "Discussion list for GROMACS users" Date: Thursday, 15 April, 2010, 1:46 PM The distortion of a protein starting structure can result from various reasons:1- experimental determination of the structure: this include the experimentalconditions (T, pH) as well as the crystal contacts if X-ray were used, dynamicsof some part of the molecule if NMR.2- the manner you solvate and equilibrate. Using position restrain on the heavy atoms of the protein first, and then on the Calphas is generally a goodidea. The time you need to run those simulations depends on the system. Ifyou see deviations you can try to run a bit longer. 100 ps is generally sufficientbut can be extended to 500 ps, this is no problem.3- the force field you are using might also trigger some "small" deviations of the protein. The protein structure might contain "strange" local configuration thatare not sable in the FF. 4- you set up, meaning time step, temperature, pressure, ... Note finally that a deviation from the starting structure might just be a fluctuationof a labile region of the protein ... On Apr 15, 2010, at 8:40 AM, sonali dhindwal wrote: Hello All, I have a protein of 576 amino acid long, and has a barell shape topolgy. I have done MD simulation on it for 1ns, and my protein has got distorted shape, i.e, one of the strand became coil and other strands became small. I wrote this query before also, can it be possible that this is due to equilibration conditons i am giving, i am equilibrating it for 100 ps under NVT using brendenson coupling. What should be ideal time for equibrating the protein with solvent ? How should it be determined, or it is based on experimenting with different conditions ? Please help. Regards. -- Sonali Dhindwal -- gmx-users mailing list gmx-us...@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...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -Inline Attachment Follows- -- gmx-users mailing list gmx-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...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- 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...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Time for equilibration
Hello All, I have a protein of 576 amino acid long, and has a barell shape topolgy. I have done MD simulation on it for 1ns, and my protein has got distorted shape, i.e, one of the strand became coil and other strands became small. I wrote this query before also, can it be possible that this is due to equilibration conditons i am giving, i am equilibrating it for 100 ps under NVT using brendenson coupling. What should be ideal time for equibrating the protein with solvent ? How should it be determined, or it is based on experimenting with different conditions ? Please help. 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-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] non-integral charge on my modeled protein structure
Sorry to bother you again but can you please help me in knowing "termini", I think total charge (i.e, cumulative) is wriiten at the last residue of a protein in [atoms] part of a .top file. that is what i have pasted in my previous mail. and Mg is in my protein, that is why 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 wrote: From: Mark Abraham Subject: Re: [gmx-users] non-integral charge on my modeled protein structure To: "Discussion list for GROMACS users" Date: Saturday, 10 April, 2010, 12:13 PM On 10/04/2010 4:08 PM, sonali dhindwal wrote: > Hello Everyone, > I have a same query, I asked before, but couldnt get a solution for that, > I have one modelled protein strucutre,,and when I run pdb2gmx to > generate topolgy file, it gives charge in non-integral value. In Then something is broken. Are your termini sane? What's that Mg doing? > terminal then it gives warning of protein having non-integral charge. > Moreover, in the toplogy file qtot for the last residue comes out to be > different than that is shown in terminal as warning. I don't believe you are looking at a .top file that corresponds to the terminal output. > I am pasting some part of end of my topology file's [atom] part here. > 4883 CH1 493 LEU CG 2100 0 13.019 ; qtot -1.94 > 4884 CH3 493 LEU CD1 2100 0 15.035 ; qtot -1.94 > 4885 CH3 493 LEU CD2 2100 0 15.035 ; qtot -1.94 > 4886 C 493 LEU C 2101 0.38 12.011 ; qtot -1.56 > 4887 O 493 LEU O 2101 -0.38 15.9994 ; qtot -1.94 > 4888 N 494 ARG N 2102 -0.28 14.0067 ; qtot -2.22 > 4889 H 494 ARG H 2102 0.28 1.008 ; qtot -1.94 > 4890 CH1 494 ARG CA 2103 0 13.019 ; qtot -1.94 > 4891 CH2 494 ARG CB 2103 0 14.027 ; qtot -1.94 > 4892 CH2 494 ARG CG 2103 0 14.027 ; qtot -1.94 > 4893 CH2 494 ARG CD 2104 0.09 14.027 ; qtot -1.85 > 4894 NE 494 ARG NE 2104 -0.11 14.0067 ; qtot -1.96 > 4895 H 494 ARG HE 2104 0.24 1.008 ; qtot -1.72 > 4896 C 494 ARG CZ 2104 0.34 12.011 ; qtot -1.38 > 4897 NZ 494 ARG NH1 2104 -0.26 14.0067 ; qtot -1.64 > 4898 H 494 ARG HH11 2104 0.24 1.008 ; qtot -1.4 > 4899 H 494 ARG HH12 2104 0.24 1.008 ; qtot -1.16 > 4900 NZ 494 ARG NH2 2104 -0.26 14.0067 ; qtot -1.42 > 4901 H 494 ARG HH21 2104 0.24 1.008 ; qtot -1.18 > 4902 H 494 ARG HH22 2104 0.24 1.008 ; qtot -0.94 > 4903 C 494 ARG C 2105 0.38 12.011 ; qtot -0.56 > 4904 O 494 ARG O 2105 -0.38 15.9994 ; qtot -0.94 > 4905 N 495 LYSH N 2106 -0.28 14.0067 ; qtot -1.22 > 4906 H 495 LYSH H 2106 0.28 1.008 ; qtot -0.94 > 4907 CH1 495 LYSH CA 2107 0 13.019 ; qtot -0.94 > 4908 CH2 495 LYSH CB 2107 0 14.027 ; qtot -0.94 > 4909 CH2 495 LYSH CG 2108 0 14.027 ; qtot -0.94 > 4910 CH2 495 LYSH CD 2108 0 14.027 ; qtot -0.94 > 4911 CH2 495 LYSH CE 2109 0.127 14.027 ; qtot -0.813 > 4912 NL 495 LYSH NZ 2109 0.129 14.0067 ; qtot -0.684 > 4913 H 495 LYSH HZ1 2109 0.248 1.008 ; qtot -0.436 > 4914 H 495 LYSH HZ2 2109 0.248 1.008 ; qtot -0.188 > 4915 H 495 LYSH HZ3 2109 0.248 1.008 ; qtot 0.06 > 4916 C 495 LYSH C 2110 0.27 12.011 ; qtot 0.33 > 4917 OM 495 LYSH O1 2110 -0.635 15.9994 ; qtot -0.305 > 4918 OM 495 LYSH O2 2110 -0.635 15.9994 ; qtot -0.94 > 4919 MG2+ 496 MG MG 2111 2 24.305 ; qtot 1.06 > > there are so many non-integral charges here for residues, > please help. No, the residues here have integral charges. The partial sum over all residues is non-integral. Go and find the first-non-integral one and fix it. Mark -- gmx-users mailing list gmx-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...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php 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-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...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] non-integral charge on my modeled protein structure
Hello Everyone, I have a same query, I asked before, but couldnt get a solution for that, I have one modelled protein strucutre,,and when I run pdb2gmx to generate topolgy file, it gives charge in non-integral value. In terminal then it gives warning of protein having non-integral charge. Moreover, in the toplogy file qtot for the last residue comes out to be different than that is shown in terminal as warning. I am pasting some part of end of my topology file's [atom] part here. 4883 CH1 493 LEU CG 2100 0 13.019 ; qtot -1.94 4884 CH3 493 LEU CD1 2100 0 15.035 ; qtot -1.94 4885 CH3 493 LEU CD2 2100 0 15.035 ; qtot -1.94 4886 C 493 LEU C 2101 0.38 12.011 ; qtot -1.56 4887 O 493 LEU O 2101 -0.38 15.9994 ; qtot -1.94 4888 N 494 ARG N 2102 -0.28 14.0067 ; qtot -2.22 4889 H 494 ARG H 2102 0.28 1.008 ; qtot -1.94 4890 CH1 494 ARG CA 2103 0 13.019 ; qtot -1.94 4891 CH2 494 ARG CB 2103 0 14.027 ; qtot -1.94 4892 CH2 494 ARG CG 2103 0 14.027 ; qtot -1.94 4893 CH2 494 ARG CD 2104 0.09 14.027 ; qtot -1.85 4894 NE 494 ARG NE 2104 -0.11 14.0067 ; qtot -1.96 4895 H 494 ARG HE 2104 0.24 1.008 ; qtot -1.72 4896 C 494 ARG CZ 2104 0.34 12.011 ; qtot -1.38 4897 NZ 494 ARG NH1 2104 -0.26 14.0067 ; qtot -1.64 4898 H 494 ARG HH11 2104 0.24 1.008 ; qtot -1.4 4899 H 494 ARG HH12 2104 0.24 1.008 ; qtot -1.16 4900 NZ 494 ARG NH2 2104 -0.26 14.0067 ; qtot -1.42 4901 H 494 ARG HH21 2104 0.24 1.008 ; qtot -1.18 4902 H 494 ARG HH22 2104 0.24 1.008 ; qtot -0.94 4903 C 494 ARG C 2105 0.38 12.011 ; qtot -0.56 4904 O 494 ARG O 2105 -0.38 15.9994 ; qtot -0.94 4905 N 495 LYSH N 2106 -0.28 14.0067 ; qtot -1.22 4906 H 495 LYSH H 2106 0.28 1.008 ; qtot -0.94 4907 CH1 495 LYSH CA 2107 0 13.019 ; qtot -0.94 4908 CH2 495 LYSH CB 2107 0 14.027 ; qtot -0.94 4909 CH2 495 LYSH CG 2108 0 14.027 ; qtot -0.94 4910 CH2 495 LYSH CD 2108 0 14.027 ; qtot -0.94 4911 CH2 495 LYSH CE 2109 0.127 14.027 ; qtot -0.813 4912 NL 495 LYSH NZ 2109 0.129 14.0067 ; qtot -0.684 4913 H 495 LYSH HZ1 2109 0.248 1.008 ; qtot -0.436 4914 H 495 LYSH HZ2 2109 0.248 1.008 ; qtot -0.188 4915 H 495 LYSH HZ3 2109 0.248 1.008 ; qtot 0.06 4916 C 495 LYSH C 2110 0.27 12.011 ; qtot 0.33 4917 OM 495 LYSH O1 2110 -0.635 15.9994 ; qtot -0.305 4918 OM 495 LYSH O2 2110 -0.635 15.9994 ; qtot -0.94 4919 MG2+ 496 MG MG 2111 2 24.305 ; qtot 1.06 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://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...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Protein is having non-integral charge
Hello All I am using gromacs for simulating my protein I got after homology modelling. While doing this when I get toplogy file by using 0: GROMOS96 43a1 force field topology file I am getting has most of the residues having non-integral charge. Can someone help in this. As far as I searched 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/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...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Distorted protein structure after MD simulation
Hello All, I have done one MD similation for 1 ns for my protein, having two ligands and one metal ion with GROMOS96 43a1 force field and dodecahedron box as tge unit cell. After simulation when i checked RMSD, it is increasing till 1ns and observing the .gro file in VMD, I have seen that, my 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. YOURS! See your Yahoo! Homepage. http://in.yahoo.com/-- 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...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
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 wrote: From: dur...@zib.de Subject: Re: [gmx-users] query regarding atom type To: "Discussion list for GROMACS users" Date: Saturday, 27 March, 2010, 8:56 PM hi there, i'm doing simulation of protein-ligand systems since a few weeks and i've been starting with a nice tutorial for acpypi (python script) http://code.google.com/p/acpypi/wiki/TutorialAcpypi4Gromacs in order to create topology-files for several (42) ligands in an automized way. works very fine so far. changes, that i've applied to the tutorial: i don't add water at the pdb2gmx step, but only later at the genbox step. in addition, i add the include line for the water topology "manually" (script). however, if you use acpypi, you should remove the coordinates/topology (section [ moleculetype ], [ atoms ], [ bonds ], ...) of the protein from the protein.top (generated by pdb2gmx) and create a own protein.itp file containing that information, which than needs to be included in the protein.top file. restriction on acpypi: number of ligand's atoms is limited to about 200 (not sure). regards, vedat > Hello All > I am trying to add ions to my protein, for that I have run this command,, > > [sak...@localhost ~/sonali]$ grompp -f ions.mdp -c protein_solv.gro -p > topol.top -o ions.tpr > and every time I run it, following error is coming > Fatal error: > Atomtype OA not found > > I am using OPLSA force field 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 Mail works best with the New Yahoo Optimized IE8. Get it NOW! > http://downloads.yahoo.com/in/internetexplorer/-- > gmx-users mailing list gmx-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...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing list gmx-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...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php 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-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...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
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 wrote: From: Justin A. Lemkul Subject: Re: [gmx-users] query regarding atom type To: "Discussion list for GROMACS users" Date: Saturday, 27 March, 2010, 8:14 PM sonali dhindwal wrote: > Hello All > I am trying to add ions to my protein, for that I have run this command,, > > [sak...@localhost ~/sonali]$ grompp -f ions.mdp -c protein_solv.gro -p > topol.top -o ions.tpr > and every time I run it, following error is coming > Fatal error: > Atomtype OA not found > > I am using OPLSA force field 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. Then you haven't been changing the right thing(s). How do you have an OA atom type in the ligand file under OPLS? What program generated your ligand .itp file? All OPLS atom types are of the format "opls_XXX," so if you've got anything else, you're dealing with some hybridized, non-functional topology that may in fact be trying to mix force fields. -Justin > > Please help > Thanks in advance > > > > -- > Sonali Dhindwal > > > > The INTERNET now has a personality. YOURS! See your Yahoo! Homepage > <http://in.rd.yahoo.com/tagline_yyi_1/*http://in.yahoo.com/>. > -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing list gmx-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...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php 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-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...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] query regarding atom type
Hello All I am trying to add ions to my protein, for that I have run this command,, [sak...@localhost ~/sonali]$ grompp -f ions.mdp -c protein_solv.gro -p topol.top -o ions.tpr and every time I run it, following error is coming Fatal error: Atomtype OA not found I am using OPLSA force field 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 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-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...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[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. YOURS! See your Yahoo! Homepage. http://in.yahoo.com/-- 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...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] query regarding neutralisation of charge on protein
Hello All, I am trying to do MD on my modelled protein and when I ran pdb2gmx command, it is showing that Total charge -12.000 e now I read in the tutorial that when there is a total charge, then we have to neutralise that charge by adding ions, but in my case it is in negative (what 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-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...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
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 wrote: From: Justin A. Lemkul Subject: Re: [gmx-users] Query regarding toplogy of Manganese ion in protein To: "Discussion list for GROMACS users" Date: Wednesday, 24 March, 2010, 5:44 PM sonali dhindwal wrote: > 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. Parameterization is considered a very advanced task, and generating good parameters for a transition metal is especially challenging. See here: http://www.gromacs.org/Documentation/How-tos/Parameterization#Exotic_Species Parameters for Mn are available for the AMBER force fields, which can be incorporated into Gromacs with the ffamber ports. The reference for Mn can be found at: http://www.pharmacy.manchester.ac.uk/bryce/amber#ion -Justin > Please Help > Regards > > -- > Sonali Dhindwal > > > > Your Mail works best with the New Yahoo Optimized IE8. Get it NOW! > <http://in.rd.yahoo.com/tagline_ie8_new/*http://downloads.yahoo.com/in/internetexplorer/>. > > -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing list gmx-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...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php The INTERNET now has a personality. YOURS! See your Yahoo! Homepage. http://in.yahoo.com/-- 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...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[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, 24/3/10, sonali dhindwal wrote: From: sonali dhindwal Subject: Query regarding toplogy of Manganese ion in protein To: gmx-users@gromacs.org Date: Wednesday, 24 March, 2010, 5:35 PM 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 Your Mail works best with the New Yahoo Optimized IE8. Get it NOW!. 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-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...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[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 The INTERNET now has a personality. YOURS! See your Yahoo! Homepage. http://in.yahoo.com/-- 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...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Fw: query regarding pdb2gmx program for protein with metal and a ligand
-- Sonali Dhindwal --- On Sun, 21/3/10, sonali dhindwal wrote: From: sonali dhindwal 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/Madam, I am new to Gromacs, and o want to run molecular dynamics study for analysis of my modelled protein which consist of a Metal Mn and a Ligand in it. But whenever I run the first step of generation of topology file through pdb2gmx program, I am getting error msg that Fatal error: Residue 'MN' not found in residue topology database So, the program fails, and I cant move forward. I tried by deleting metal and ligand from my protein, then it is working, but I have to consider Metal and ligand. I searched on google also, regarding this error, but couldnt get through this problem, so please help. Thanks in advance. Regards -- Sonali Dhindwal Your Mail works best with the New Yahoo Optimized IE8. Get it NOW!. 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-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...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
