Re: [gmx-users] TFE-water simulation

Hello again, That depends on the peptide. There is no general answer. I am starting with a linear conformations, but that's because I'm working with intrinsically disordered proteins. That's as far as I can go regarding telling you about what I'm doing. I'm not at liberty to discuss these things,

Re: [gmx-users] TFE-water simulation

Should I start with helical peptides and see if it maintains the helicity or I can start with random coil? Do random coil peptides take long simulation time to form helical peptides? any help on this will be appreciated. On Tue, Nov 5, 2013 at 12:25 AM, Archana Sonawani-Jagtap < ask.arch...@gma

Re: [gmx-users] TFE-water simulation

Thanks Joao Henriques for helping me with the steps. On Nov 4, 2013 3:18 PM, "João Henriques" wrote: > Hello Archana, > > I'm also toying with a TFE-water system, therefore I am also a newbie. This > is what I am doing, I hope it helps: > > 1) Since I'm using G54A7 I created a TFE.itp using GROMO

Re: [gmx-users] TFE-water simulation

Erratum: Where I wrote "I ended up going with the former" it should be "I ended up going with the latter". /J On Mon, Nov 4, 2013 at 10:47 AM, João Henriques < joao.henriques.32...@gmail.com> wrote: > Hello Archana, > > I'm also toying with a TFE-water system, therefore I am also a newbie. > T

Re: [gmx-users] TFE-water simulation

Hello Archana, I'm also toying with a TFE-water system, therefore I am also a newbie. This is what I am doing, I hope it helps: 1) Since I'm using G54A7 I created a TFE.itp using GROMOS parameters (I don't use PRODGR, see why in DOI: 10.1021/ci100335w). 2) Do the math and check how many molecules

Re: [gmx-users] TFE-water simulation

On 10/24/13 1:13 PM, Archana Sonawani-Jagtap wrote: Dear Justin, I have not constructed the system but I have downloaded it from ATB website. To maintain the number of TFE and water molecules(1:1 v/v) in the system (I don't want to add extra water molecules) I tried many options in genbox but

Re: [gmx-users] TFE-water simulation

Dear Justin, I have not constructed the system but I have downloaded it from ATB website. To maintain the number of TFE and water molecules(1:1 v/v) in the system (I don't want to add extra water molecules) I tried many options in genbox but still it adds 678 water molecules. Can you provide me so

Re: [gmx-users] TFE-water simulation

On 10/23/13 7:20 AM, Archana Sonawani-Jagtap wrote: Hi all, I have never performed TFE-water simulation therfore I want to know after inserting the peptide in the pre-equilibrated TFE-water mixture, do we need to adjust the number of TFE or water molecules ? That depends on how you construc

[gmx-users] TFE-water simulation

Hi all, I have never performed TFE-water simulation therfore I want to know after inserting the peptide in the pre-equilibrated TFE-water mixture, do we need to adjust the number of TFE or water molecules ? or should I directly add ions to this system and run the production run. Any suggestion i

Re: [gmx-users] TFE-water simulation

On 7/17/13 6:26 AM, Archana Sonawani-Jagtap wrote: Hi Justin, Thanks...it was really helpful. I saw the http://www.gromacs.org/Documentation/How-tos/Mixed_Solvents site. Now I don't know how to calculate the number of cosolvents (in my case TFE for TFE-water in 1:1 vol). Is there any formula

Re: [gmx-users] TFE-water simulation

Hi Justin, Thanks...it was really helpful. I saw the http://www.gromacs.org/Documentation/How-tos/Mixed_Solvents site. Now I don't know how to calculate the number of cosolvents (in my case TFE for TFE-water in 1:1 vol). Is there any formula to carry out this calculation. I can follow other menti

Re: [gmx-users] TFE-water simulation

On 7/17/13 1:03 AM, Archana Sonawani-Jagtap wrote: HI, I want to simulate helical peptide in TFE-water (1:1 vol) solvent. 1. From previous searches, I got to know that tfe.itp is present in gmx.ff folder. Can I use this itp file by including it in my top file generated during pdb2gmx. Sinc

[gmx-users] TFE-water simulation

HI, I want to simulate helical peptide in TFE-water (1:1 vol) solvent. 1. From previous searches, I got to know that tfe.itp is present in gmx.ff folder. Can I use this itp file by including it in my top file generated during pdb2gmx. 2. I also got TFE-water (1:1 vol) pdb and gro pre-equilibrate

Re: [gmx-users] TFE Proper Dihedral types...

On 5/16/12 12:36 AM, rama david wrote: On Tue, May 15, 2012 at 10:24 PM, Justin A. Lemkul mailto:jalem...@vt.edu>> wrote: The parameters are missing from ffbonded.itp, making the implementation incomplete. You can obtain a TFE topology from ATB: http://compbio.biosci.uq.edu.

Re: [gmx-users] TFE Proper Dihedral types...

On Tue, May 15, 2012 at 10:24 PM, Justin A. Lemkul wrote: > > > > The parameters are missing from ffbonded.itp, making the implementation > incomplete. You can obtain a TFE topology from ATB: > > http://compbio.biosci.uq.edu.**au/atb/download.py?molid=1655

Re: [gmx-users] TFE Proper Dihedral types...

On 5/15/12 12:14 PM, rama david wrote: Hi Gromacs Friends .. I am using TFE (Trifluro Ethanol ) as a solvent for my simulation study.. I am using G96 53a6 ff After the genbox -cp .. -cs tef.pdb -o mix.pdb I count the no of solvent molecule , to update topology .. after Grompp I am facing fo

[gmx-users] TFE Proper Dihedral types...

Hi Gromacs Friends .. I am using TFE (Trifluro Ethanol ) as a solvent for my simulation study.. I am using G96 53a6 ff After the genbox -cp .. -cs tef.pdb -o mix.pdb I count the no of solvent molecule , to update topology .. after Grompp I am facing following error grompp -f minim.mdp -c mix.pd

Re: [gmx-users] tfe and gromos9653a

shahrbanoo karbalaee wrote: Dear justin I guess I did right.I add in my topoly file tfe in part of dehedrals " gd_24".(from your edit in dmso topolgy last another mail)and I could minimize. what do you think this adding ?.any way thank you for every thing.now about my peptide I have this e

[gmx-users] tfe and gromos9653a

Dear justin I guess I did right.I add in my topoly file tfe in part of dehedrals " gd_24".(from your edit in dmso topolgy last another mail)and I could minimize. what do you think this adding ?.any way thank you for every thing.now about my peptide I have this error .(in c terminal peptide i

Re: [gmx-users] tfe

shahrbanoo karbalaee wrote: Dear justin for have tfe30% after I got tfedrg.top with pdb2gmx and force field gromos965a. I do t this command : editconf -f tfedrg.gro -bt dodecahedron -d 0.71 -o box.gro genbox -cp box.gro -cs spc216.gro ci tfedrg.gro - nmol 40 -p topol.top -o solvated.gro I

[gmx-users] tfe

Dear justin for have tfe30% after I got tfedrg.top with pdb2gmx and force field gromos965a. I do t this command : editconf -f tfedrg.gro -bt dodecahedron -d 0.71 -o box.gro genbox -cp box.gro -cs spc216.gro ci tfedrg.gro - nmol 40 -p topol.top -o solvated.gro I did that command with spc.gro(I

Re: [gmx-users] tfe

shahrbanoo karbalaee wrote: Dear justin as your telling I have two way for my problem: 1-choose force field that is compatible to TFE(with 7 atom) that I used another force field.I made tfe.pdb (with 7 atom) and choose gromos 96 but I got error that dont found HO atom. Are you trying to creat

[gmx-users] tfe

Dear justin as your telling I have two way for my problem: 1-choose force field that is compatible to TFE(with 7 atom) that I used another force field.I made tfe.pdb (with 7 atom) and choose gromos 96 but I got error that dont found HO atom. 2)another way,I must itp file for tfe with opls forcefiel

Re: [gmx-users] tfe

Comments are embedded throughout. There are several errors, some related to your problem, and others that you should definitely fix before you expect to run any real dynamics. shahrbanoo karbalaee wrote: Dear justin here it is. creating statusfile for 1 node... Back Off! I just backed up

[gmx-users] tfe

Dear justin here it is. creating statusfile for 1 node... Back Off! I just backed up mdout.mdp to ./#mdout.mdp.6# WARNING 1 [file em.mdp, line unknown]: Unknown left-hand 'constrains' in parameter file WARNING 2 [file em.mdp, line unknown]: Unknown left-hand 'nslist' in parameter file check

Re: [gmx-users] tfe

shahrbanoo karbalaee wrote: Dear justin I trap in local minma.I dont know. I don't know either. Do you think there is some problem with your minimization? What happened when you minimized your structure? Now after edit topolgy file I get error again.not found C type.I make tfe.pdb and t

[gmx-users] tfe

Dear justin I trap in local minma.I dont know. Now after edit topolgy file I get error again.not found C type.I make tfe.pdb and tfe.gro in prodrg and try it again editconf for change pdb to gro file. I saw source code toputil line 61.not found C type. best-- sh-karbalaee __

Re: [gmx-users] tfe

shahrbanoo karbalaee wrote: ; Include Position restraint file #ifdef POSRES #include "posre.itp" ; Include water topology #include "spce.itp" Include tfe topology #include "tfe.itp" #endif Well, there's the problem. You've enclosed the SPC/E and TFE .itp files within an #ifdef/#endif blo

[gmx-users] tfe

Dear justin I try again .but I get this error toputil .line 1364 not found such molecoule SOL.then would you please check my topol.top file and advise me. PEPTIDE A5 OR AUREIN 1.2 ; ; Include forcefield parameters #include "ffoplsaa.itp" [ moleculetype ] ; Namenrexcl Protein_A

Re: [gmx-users] tfe

shahrbanoo karbalaee wrote: Dear justin and mark hi again I work in tfe.pdb with polar hydrogen from prodrg.and with commnad genbox -cp -- ci tfe.gro -nmol 50 -o mtfe.gro ANDcommand genbox -cp mtfe.gro -cs -out2 make the file peptide ,tfe ,water .then by change number the mole it wil

[gmx-users] tfe

Dear justin and mark hi again I work in tfe.pdb with polar hydrogen from prodrg.and with commnad genbox -cp -- ci tfe.gro -nmol 50 -o mtfe.gro ANDcommand genbox -cp mtfe.gro -cs -out2 make the file peptide ,tfe ,water .then by change number the mole it will make 30%.and edit topology fil

Re: [gmx-users] tfe

shahrbanoo karbalaee wrote: Dear mark and justin hi,thank you for your advices. I want to make simulation peptide in 30%tfe.I get tfe.pdb and take tfe.gro from prodrug program.I make solvatedtfe.gro and the other solvatedspc.gro.then I make 30mol tfe and 70 spc in a file by hands.and then run g

[gmx-users] tfe

Dear mark and justin hi,thank you for your advices. I want to make simulation peptide in 30%tfe.I get tfe.pdb and take tfe.gro from prodrug program.I make solvatedtfe.gro and the other solvatedspc.gro.then I make 30mol tfe and 70 spc in a file by hands.and then run genbox -f .cs 3tfe70spc.gro .

Re: [gmx-users] TFE in molecular dynamic

Luisa Calvanese wrote: How become part TFE molecules in a calculation of molecular dynamics? Please see http://www.catb.org/~esr/faqs/smart-questions.html Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listin

[gmx-users] TFE in molecular dynamic

How become part TFE molecules in a calculation of molecular dynamics? _ Ti piace giocare con le lettere? Prova ABCLive! http://messengergiochi.it.msn.com/___ gmx-users mailing listgmx-u

[gmx-users] TFE in molecular dynamic

How become part TFE molecules in a calculation of molecular dynamics? _ Scarica GRATIS la versione personalizzata MSN di Internet Explorer 7! http://optimizedie7.msn.com/default.aspx?mkt=it-it_

Re: [gmx-users] TFE query

Dilraj Lama wrote: Hello gmx users, I have a query and would be greatfull if I could get some suggestions on the subject. I constructed a "tfe.itp" file with the parameters mentioned by Fioroni et. al., J. Phys. Chem. B 2000, 104, 12347-12354. I then gen

[gmx-users] TFE query

Hello gmx users, I have a query and would be greatfull if I could get some suggestions on the subject. I constructed a "tfe.itp" file with the parameters mentioned by Fioroni et. al., J. Phys. Chem. B 2000, 104, 12347-12354. I then generated a "tfe.gro" fi

Re: [gmx-users] TFE solvent box

I think replace HO by OA chiradip --- [EMAIL PROTECTED] wrote: > Hi all, > > We want to create and simulate a solvent box > containing TFE. We have > already generated the TFE.gro file, and by using > this file we created > a box containing 38 molecules of TFE (TFE_solv.gro). > We created a

Re: [gmx-users] TFE solvent box

[EMAIL PROTECTED] wrote: Hi all, We want to create and simulate a solvent box containing TFE. We have already generated the TFE.gro file, and by using this file we created a box containing 38 molecules of TFE (TFE_solv.gro). We created a file TFE.top including the tfe topology (using tfe.itp,

[gmx-users] TFE solvent box

Hi all, We want to create and simulate a solvent box containing TFE. We have already generated the TFE.gro file, and by using this file we created a box containing 38 molecules of TFE (TFE_solv.gro). We created a file TFE.top including the tfe topology (using tfe.itp, provided by GROMACS)

Re: [gmx-users] TFE-water minimization

Owen, Michael wrote: Hello, I have created my own TFE.itp file for a mixed solvent simulation containing TFE and TIP4P water. To test my TFE file I put one TFE molecule in a box of solvent and and tried to minimize it using the following parameters: define = -DPOSRES cpp

[gmx-users] TFE-water minimization

Hello, I have created my own TFE.itp file for a mixed solvent simulation containing TFE and TIP4P water. To test my TFE file I put one TFE molecule in a box of solvent and and tried to minimize it using the following parameters: define = -DPOSRES cpp = /lib/cp

Re: [gmx-users] TFE .gro files

Copps, Jeffrey wrote: Hello all, Does anyone have TFE (trifluoroethanol) .gro files that they might be willing to share? Or, barring that, can anyone tell me how to create a solvent .gro file? Much thanks, Jeff Copps --

[gmx-users] TFE .gro files

Title: TFE .gro files Hello all, Does anyone have TFE (trifluoroethanol) .gro files that they might be willing to share?  Or, barring that, can anyone tell me how to create a solvent .gro file? Much thanks, Jeff Copps ___