[gmx-users] Regarding Pulling simulation:To study the base flipping of the thymine
Hi all, I am studying a system which consists of DNA duplex 20 base pairs. Actually I am interested in studying the base flipping of the thymine. I have the crystal structure of extrahelical DNA in which thymine is out side the helical structure. I want use pulling simulations to bring this base from extrahelical to Intrahelical conformation, is there any way to do it in GROMACS pull code. Please see the figure below (link) for description. http://researchweb.iiit.ac.in/~kartheek.p/extrintra.png -- Thanks and Regards, kartheek, -- 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] Topology and mdp file for coupling vdw and coulombic interactions for running FE calculations using BAR
Hi, I'm preparing my mdp and topology files for running free energy calculations using BAR method. I´m using Justin Lemkul's tutorial as a reference (You can find it here http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/free_energy/08_advanced.html). According to this tutorial, the simultaneous coupling of both Coulombic and van der Waals terms leads to instability. So, it is usefull to prepare the mdp files as follows (off course including all other parameters): van der Waals coupling: sc-alpha = 0.5 ; use soft-core for LJ (de)coupling sc-sigma = 0.3 sc-power = 1 couple-moltype= LIG couple-intramol = no couple-lambda0= none; non-interacting dummy in state A couple-lambda1= vdw ; only vdW terms on in state B Coulombic coupling: sc-alpha = 0 ; soft-core during (dis)charging can be unstable! sc-sigma = 0 couple-moltype= LIG couple-intramol = no couple-lambda0= vdw ; only vdW terms in state A (the previous state B is now A) couple-lambda1= vdw-q ; all nonbonded interactions are on in state B However, I don't understand how can this leads to a fully interacting molecule if all the charges in the topology file have been set to zero. Does it mean that for the second calculation (coulombic coupling) I have to use the original topology file with all charges? Or, should I use the same topology with zero charges? Thanks in advance, Sonia Aguilera Graduate student-Chemical Engineering Department Universidad de los Andes Colombia -- 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] About topology construction for Cyclic peptide
Dear Mark, Thank you for your reply I have used the peptide FLF For that pdb2gmx construct topology successfully with -ter choosing any thing for both terminal. But When i Choose none with -ter for both terminal It again shows error as follows Fatal error: There is a dangling bond at at least one of the terminal ends. Select a proper terminal entry. For your Convenience i have pasted the previous discussion That suggests you have a problem with your coordinate file that is independent of your attempt to cyclize. Can you generate a topology for FL with a) -ter choosing none, b) -ter choosing anything else? With Regards S.vidhyasankar -- 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] About topology construction for yclic pepetide
On 17/09/2012 2:55 AM, vidhya sankar wrote: Dear Mark , AgainThanks for you reply After Editing my pdb file from intial FL to FLF format Then i Run pdb2gmx for my linaerpdb file , i have selected none for both termini ( with -ter option) as you mailed me in the previous mail I have got error as follows Fatal error: There is a dangling bond at at least one of the terminal ends. Select a proper terminal entry. How to Rectify this error That suggests you have a problem with your coordinate file that is independent of your attempt to cyclize. Can you generate a topology for FL with a) -ter choosing none, b) -ter choosing anything else? Mark For your Remembrance i pasted your previous Discussion 1) Take your initial coordinate file, make a copy and in it make a copy of the first residue and place it after the last residue, taking care to obey the format of the file you're using, and update things like atom counts and atom and residue indices. The coordinates of the copied atoms don't matter. Now you have a coordinate file for FLF. 2) Process that with pdb2gmx using -ter and choosing "none". This has built a linear topology for FLF, with a correct L-to-F link for you to use as a template for making a cyclic FL. Thanks in Advance -- 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] About topology construction for yclic pepetide
Dear Mark , Again Thanks for you reply After Editing my pdb file from intial FL to FLF format Then i Run pdb2gmx for my linaer pdb file , i have selected none for both termini ( with -ter option) as you mailed me in the previous mail I have got error as follows Fatal error: There is a dangling bond at at least one of the terminal ends. Select a proper terminal entry. How to Rectify this error For your Remembrance i pasted your previous Discussion 1) Take your initial coordinate file, make a copy and in it make a copy of the first residue and place it after the last residue, taking care to obey the format of the file you're using, and update things like atom counts and atom and residue indices. The coordinates of the copied atoms don't matter. Now you have a coordinate file for FLF. 2) Process that with pdb2gmx using -ter and choosing "none". This has built a linear topology for FLF, with a correct L-to-F link for you to use as a template for making a cyclic FL. Thanks in Advance -- 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] lipid-protein simulation
On 9/16/12 12:48 PM, Shima Arasteh wrote: Thanks. Yes, I want to use the coordinate file from 50-ns simulation. Would you please let me know what the criterion for knowing that the equilibrated system is proper for insertion of protein? Do the temperature, RMSD, pressure and visualization of popc-water system make me decide that it is a proper system or not? None of those criteria are specific enough, in my opinion. Lipid-specific metrics like area per lipid, membrane thickness, lateral diffusion, etc should all be considered. There is a wealth of literature that exists about membrane simulations from which you can draw ideas. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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 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] lipid-protein simulation
Thanks. Yes, I want to use the coordinate file from 50-ns simulation. Would you please let me know what the criterion for knowing that the equilibrated system is proper for insertion of protein? Do the temperature, RMSD, pressure and visualization of popc-water system make me decide that it is a proper system or not? Thanks for your suggestions dear Justin. Sincerely, Shima From: Justin Lemkul To: Shima Arasteh ; Discussion list for GROMACS users Sent: Sunday, September 16, 2012 9:08 PM Subject: Re: [gmx-users] lipid-protein simulation On 9/16/12 12:34 PM, Shima Arasteh wrote: > > > Dear all, > > To simulate a lipid-protein system, I'm using CHARMM36 FF and popc lipid > bilayer. So I need to put popc.pdb, popc.itp and lipid.itp files in my > working directory. I'm wondering: > 1.if it is correct to use popc.itp generated from 50 ns-simulated popc in >water? I will assume you mean the coordinate file is from a 50-ns simulation? Topologies are not time-dependent. If you can demonstrate that your membrane is properly equilibrated in this time frame, then yes, it is a plausible starting model. > 2. I need to have lipid.itp defined by C36 FF. Would it be correct to get an > individual popc.pdb and generate lipid.itp by pdb2gmx? I'm not sure about > this way of generating lipid.itp, so please give me your suggestions. > If you already have popc.itp then you don't need to run pdb2gmx. What is lipid.itp? If you're somehow thinking you need the Berger lipid parameters from Peter Tieleman, you don't. CHARMM36 was built to handle lipids, so all necessary atom types, nonbonded, and bonded parameters should already be present in the force field, thus requiring no external modification. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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 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] lipid-protein simulation
On 9/16/12 12:34 PM, Shima Arasteh wrote: Dear all, To simulate a lipid-protein system, I'm using CHARMM36 FF and popc lipid bilayer. So I need to put popc.pdb, popc.itp and lipid.itp files in my working directory. I'm wondering: 1.if it is correct to use popc.itp generated from 50 ns-simulated popc in water? I will assume you mean the coordinate file is from a 50-ns simulation? Topologies are not time-dependent. If you can demonstrate that your membrane is properly equilibrated in this time frame, then yes, it is a plausible starting model. 2. I need to have lipid.itp defined by C36 FF. Would it be correct to get an individual popc.pdb and generate lipid.itp by pdb2gmx? I'm not sure about this way of generating lipid.itp, so please give me your suggestions. If you already have popc.itp then you don't need to run pdb2gmx. What is lipid.itp? If you're somehow thinking you need the Berger lipid parameters from Peter Tieleman, you don't. CHARMM36 was built to handle lipids, so all necessary atom types, nonbonded, and bonded parameters should already be present in the force field, thus requiring no external modification. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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 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] lipid-protein simulation
Dear all, To simulate a lipid-protein system, I'm using CHARMM36 FF and popc lipid bilayer. So I need to put popc.pdb, popc.itp and lipid.itp files in my working directory. I'm wondering: 1.if it is correct to use popc.itp generated from 50 ns-simulated popc in water? 2. I need to have lipid.itp defined by C36 FF. Would it be correct to get an individual popc.pdb and generate lipid.itp by pdb2gmx? I'm not sure about this way of generating lipid.itp, so please give me your suggestions. Would you please help me? Thanks in advance. Sincerely, Shima -- 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: RE: [gmx-users] energy minimisation of carbon nanotubes.
I recommend use the double precision just to check the better result to your system. In my case, i've got much better results using emtol=0.004 and double precision. My system is too much unstable and i tried. I have no regrets... Marcelo Depolo Em 15/09/2012 22:11, "Elie M" escreveu: Thank you for your reply and help. Regards Elie > Date: Sat, 15 Sep 2012 13:32:06 -0400 > From: jalem...@vt.edu > To: gmx-users@gromacs.org > Subject: Re: [gmx-users] energy minimisation of carbon nanotubes. > > > > On 9/15/12 12:49 PM, Elie M wrote: > > > > Dear all, > > I have a small question regardin... -- 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] g_confrms
On 17/09/2012 12:10 AM, Ankita naithani wrote: Hi Mark, I haven't been able to figure out the reason of the difference between the two structures. When I prompt for my backbone to be fitted against each other, the initial structure has 2965 elements and the final output file has 2955 elements. Could you please suggest the possible reason for the difference? Somewhere between "initial" and "final" you changed the composition. Only you know what what those states were and what you did between them :-) Mark On Sun, Sep 16, 2012 at 3:03 PM, Mark Abraham wrote: On 16/09/2012 11:49 PM, Ankita naithani wrote: Hi, I am trying to use g_confrms to compare my initial and final structure and fit them on their backbone. However, I notice a difference of 10 atoms in both of these structures and so I am unable to use g_confrms. Can anyone please help me and advice me regarding this as the manual does mention about using g_confrms irrespective of the number of atoms. Why are the two things you are trying to compare not the same? Mark -- 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 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] g_confrms
Hi Mark, I haven't been able to figure out the reason of the difference between the two structures. When I prompt for my backbone to be fitted against each other, the initial structure has 2965 elements and the final output file has 2955 elements. Could you please suggest the possible reason for the difference? On Sun, Sep 16, 2012 at 3:03 PM, Mark Abraham wrote: > On 16/09/2012 11:49 PM, Ankita naithani wrote: >> >> Hi, >> >> I am trying to use g_confrms to compare my initial and final structure >> and fit them on their backbone. However, I notice a difference of 10 >> atoms in both of these structures and so I am unable to use g_confrms. >> Can anyone please help me and advice me regarding this as the manual >> does mention about using g_confrms irrespective of the number of >> atoms. > > > Why are the two things you are trying to compare not the same? > > Mark > -- > 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 -- Ankita Naithani -- 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] g_confrms
On 16/09/2012 11:49 PM, Ankita naithani wrote: Hi, I am trying to use g_confrms to compare my initial and final structure and fit them on their backbone. However, I notice a difference of 10 atoms in both of these structures and so I am unable to use g_confrms. Can anyone please help me and advice me regarding this as the manual does mention about using g_confrms irrespective of the number of atoms. Why are the two things you are trying to compare not the same? Mark -- 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] g_confrms
Hi, I am trying to use g_confrms to compare my initial and final structure and fit them on their backbone. However, I notice a difference of 10 atoms in both of these structures and so I am unable to use g_confrms. Can anyone please help me and advice me regarding this as the manual does mention about using g_confrms irrespective of the number of atoms. Best Wishes, -- Ankita Naithani -- 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
