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

Re: [gmx-users] TFE-water simulation

at 7:15 PM, Justin Lemkul jalem...@vt.edu wrote: 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

[gmx-users] TFE-water simulation

is welcome. Thank you. -- Archana Sonawani-Jagtap Senior Research Fellow, Biomedical Informatics Centre, NIRRH (ICMR), Parel Mumbai, India. 9960791339 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http

[gmx-users] Bilayer thickness error

without peptide) When running in Gnuplot I get following error: splot 'output.frame1.20x20.average_thickness.dat' matrix using (1+$1):(1+$2):3 Warning: empty x range [1:1], adjusting to [0.99:1.01] Please help me. -- Archana Sonawani-Jagtap Senior Research Fellow, Biomedical Informatics Centre

Re: [gmx-users] Bilayer thickness error

thank you so much. It was such a stupid error from my side. On Fri, Oct 18, 2013 at 5:08 PM, Justin Lemkul jalem...@vt.edu wrote: On 10/18/13 2:54 AM, Archana Sonawani-Jagtap wrote: Hi, This is my input file for calculating bilayer thickness in absence of peptide: ## Input file

[gmx-users] lipid tail order

manner as Justin's KALP tutorial skipping the peptide insertion part? Please help me... thanks in advance -- Archana Sonawani-Jagtap Senior Research Fellow, Biomedical Informatics Centre, NIRRH (ICMR), Parel Mumbai, India. 9960791339 -- gmx-users mailing listgmx-users@gromacs.org http

[gmx-users] (no subject)

to output.frame1.200x198.bottom_a reas.dat -- Archana Sonawani-Jagtap Senior Research Fellow, Biomedical Informatics Centre, NIRRH (ICMR), Parel Mumbai, India. 9960791339 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive

[gmx-users] Bilayer thickness

the lateral area of system and APL.(keeping thickness as no) which lateral area has to be considered as the thickness of the bilayer in terms of nm? both have different values. I am confused. which values should be reported for thickness and APL? Please help me. -- Archana Sonawani-Jagtap

[gmx-users] pair distribution function

to calculate the center of mass for a bilayer? Any help is highly appreciated. -- Archana Sonawani-Jagtap Senior Research Fellow, Biomedical Informatics Centre, NIRRH (ICMR), Parel Mumbai, India. 9960791339 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx

Re: [gmx-users] pair distribution function

Thank you. On Sun, Oct 6, 2013 at 8:12 PM, Justin Lemkul jalem...@vt.edu wrote: On 10/6/13 10:36 AM, Archana Sonawani-Jagtap wrote: I have simulations for different peptides in POPC bilayer. I want to calculate pair distribution function (pdf) between negatively charged phosphate

Re: [gmx-users] TFE-water simulation

mentioned steps. Thanks in advance. On Wed, Jul 17, 2013 at 2:41 PM, Justin Lemkul jalem...@vt.edu wrote: 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

[gmx-users] TFE-water simulation

-equilibrated system from ATB site. I dont know if I can use either this pdb or gro file during genbox step for -cs flag Can anyone help me out in this regard. Thanks in advance. Regards, Archana Sonawani-Jagtap Senior Research Fellow, Biomedical Informatics Centre, NIRRH (ICMR), Parel Mumbai, India

[gmx-users] delta G of binding for protein-ligand complex

to perform (de)coupling of the ligand in complex with the receptor and in bulk solution. I don't know exactly how to start with this process. Do I need only the protein-ligand complex simulated for 5ns to start with? Thanks in advance. -- Archana Sonawani-Jagtap Junior Research Fellow, Biomedical

Re: [gmx-users] distance between protein and ligand

? I also asked the similar question. Alex replied : I would start several (5-10?) runs with different (random) starting impulse to get more reliable data. Best Shiyong On Tue, Oct 9, 2012 at 12:48 PM, Archana Sonawani ask.arch...@gmail.com wrote: Hi, I have simulated a protein

[gmx-users] distance between protein and ligand

is around 6.3 nm2 throughout the simulation which is very high. This is very contradicting result. Is something wrong in the simulation? Thanks in advance. -- Archana Sonawani-Jagtap Junior Research Fellow, Biomedical Informatics Centre, NIRRH (ICMR), Parel Mumbai, India. 9960791339 -- gmx-users

Re: [gmx-users] Umbrella sampling-protein-ligand complex

at 8:00 PM, Justin Lemkul jalem...@vt.edu wrote: On 9/28/12 9:27 AM, Archana Sonawani wrote: Hi, I have performed simulations for 3 different ligands complexed with the same protein. I want to compare the binding energies of these different three complexes. Will umbrella sampling be useful

Re: [gmx-users] energy minimization output

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 -- Archana

Re: [gmx-users] Regarding RMSD analysis result

Hi, Your RMSD graph is ok but is represented wrong due to pbc problem. Use whole and nojump options of trjconv. On Tue, Sep 25, 2012 at 2:15 PM, Felipe Pineda, PhD luis.pinedadecas...@lnu.se wrote: On 09/25/2012 10:08 AM, naga sundar wrote: Dear Felipe Thanks for ur

Re: [gmx-users] do_dssp segmental fault

://www.gromacs.org/Support/Mailing_Lists -- Archana Sonawani-Jagtap Junior Research Fellow, Biomedical Informatics Centre, NIRRH (ICMR), Parel Mumbai, India. 9960791339 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive

[gmx-users] Topology error

Dear Sir/Madam, For orienting the protein and membrane, I have used the .mdp and following topology file: ; ; File 'topol_popc.top' was generated ; By user: jalemkul (502) ; On host: bevany.biochem.vt.edu ; At date: Fri Oct 20 13:26:53 2006 ; ; This is your topology

[gmx-users] Ligand charge assignment

Dear Sir/madam, I have a ligand molecule for which I generated the topology file using Prodrg software. As the charges and groupings provided by Prodrg are not much reliable. I need to assign correct charges and groupings for my ligand. I had referred the article Practical considerations for

[gmx-users] Query for RMSD

Hello, I have run 10 ns simulation for ligand-receptor complex. For analysis, I checked RMSD, Radius of gyration, Hydrogen bonds and distance using g_dist. In the RMSD plot, the whole simulation shows RMSD between 0 - 0.5nm , but after 5ns I get long vertical lines upto 2.5 nm. I dont know whats

[gmx-users] Re:binding energy

Hi, I am performing MD simulations for peptide(ligand)-receptor complex. I dont know how to calculate the binding energy for the complex and individual structures using gromacs version 4. Can anyone please help me out. Regards, Archana. ___