[gmx-users] Glycosylation of ASN

Hi, Have you tried reducing the timestep in mdp? Yes, I tried. But no hope. On Mon, May 4, 2020, 2:52 AM Naba https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users>> wrote: >* Dear users and developers, *>>* I have spent extensive amount of time to model glycosylat

[gmx-users] Glycosylation of ASN

the structure several times using other software including a series of vacuum minimization with GROMACS-2019.5 using steepest descent and conjugate gradient minimizers. But no success. Please try to give a way to resolve it. If possible. Regards, Naba Nabajyoti Goswami Research Associate

[gmx-users] Water permeation through a channel of membrane protein

s my gro file: https://www.dropbox.com/l/scl/AACHT3J_YHEPyPSQRWn2YOmaUNwRY1eRPQw Regards Naba Nabajyoti Goswami Bioinformatics Infrastructure Facility Department of Animal Biotechnology College of Veterinary Science Khanapara,Guwahati 781022 Assam, India -- Gromacs Users mailing list * Pl

[gmx-users] Combining position restraints with Parrinello-Rahman pressure coupling leads to instabilities

output. So, I can proceed with Berendsen pressure coupling, am I right? Thanks & regards, Naba On 8/20/18 6:52 AM, Naba wrote: > > Dear Gromacs users and developers, > > > > I am using Gromacs 2018.2. > > Following the membrane protein simulation tutorial, I

[gmx-users] Combining position restraints with Parrinello-Rahman pressure coupling leads to instabilities

Dear Gromacs users and developers, I am using Gromacs 2018.2. Following the membrane protein simulation tutorial, I am planning to run long simulations of a tetramer that needs larger lipid bilayer than 128 lipids as described in the tutorial. So, I have replicated the pre-equilibrated POPC

Re: [gmx-users] Pulling two groups in opposite direction

> > On 5/17/18 1:39 AM, Naba wrote: > >> On 5/16/18 3:32 AM, Naba wrote: > >>> Dear all, > >>> > >>> I am using gromacs 5.1.2 and trying to pull both monomers of 128 amino > >>> acids from its homodimer in opposite directions along

Re: [gmx-users] Pulling two groups in opposite direction

On Thu, May 17, 2018 at 11:09 AM, Naba <nabajyoti.gosw...@gmail.com> wrote: > On 5/16/18 3:32 AM, Naba wrote: >> > Dear all, >> > >> > I am using gromacs 5.1.2 and trying to pull both monomers of 128 amino >> > acids from its homodimer in opposite

Re: [gmx-users] Pulling two groups in opposite direction

> > On 5/16/18 3:32 AM, Naba wrote: > > Dear all, > > > > I am using gromacs 5.1.2 and trying to pull both monomers of 128 amino > > acids from its homodimer in opposite directions along z axis. The > > interfaces of each protein chain is parallel to the z ax

[gmx-users] Pulling two groups in opposite direction

Dear all, I am using gromacs 5.1.2 and trying to pull both monomers of 128 amino acids from its homodimer in opposite directions along z axis. The interfaces of each protein chain is parallel to the z axis. I do not need any restraints in this case. I have gone through the GROMACS manual and some

[gmx-users] COM pulling

Dear users, Please let me know whether it is feasible and relevant or not if I use COM pulling for mechanical unfolding of proteins. More specifically, whether I can define the two group within the same molecule !! Sorry for the previous mail as it was wrongly sent to an unrelated thread. --

Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 160, Issue 74

Dear users, Please let me know whether it is feasible and relevant or not if I use COM pulling for mechanical unfolding of proteins. More specifically, whether I can define the two group within the same molecule !! On Wed, Aug 16, 2017 at 6:48 AM, <

Re: [gmx-users] Dynamic Cross Correlation

Hi, you can compute dynamic cross correlation using Bio3D package within R. Follow this link: http://thegrantlab.org/bio3d/tutorials/trajectory-analysis Regards, Naba On Sat, Oct 17, 2015 at 4:14 AM, ANAND AMITKUMAR Dharia < adha...@berkeley.edu> wrote: > Hello, > > Is t

Re: [gmx-users] Regarding gmx-user mailing list thread "Gibbs free energy landscape Vs. the stability of protein structure"

Dear David sir, Is it feasible to evaluate Gibbs free energy landscape of only the concerned loops from cartesian coordinates? I mean to say is it feasible to extract covariance matrix of my concerned loops from the entire trajectory and then evaluating Gibbs free energy landscape? OR, should I

[gmx-users] Gibbs free energy landscape Vs. the stability of protein structure

Dear Gromacs users and Developers, I have performed dihedral PCA for 4 extracellular loops of a transmembrane protein after successfully finishing 100 ns of simulation at 300 and 310 K. I obtained figures for each loops for two different temperatures as in this link:

Re: [gmx-users] Gibbs free energy landscape Vs. the stability of protein structure

Thank you Justin. I have to deduce some inference from this figure. Please make me out about the following queries. On Mon, Sep 21, 2015 at 5:48 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 9/21/15 4:00 AM, Naba wrote: > >> Dear Gromacs users and Developers

Re: [gmx-users] g_sham

University of Tennessee/Oak Ridge National Laboratory Center for Molecular Biophysics From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Naba nabajyoti.gosw...@gmail.com Sent: Saturday

Re: [gmx-users] g_sham

. It says ^ unexpected newline or end of string. I have supplied my coord1min, coord2min, yourfile_first_coordinate_here.xvg and yourfile_second_coordinate_here.xvg. can you please re-write the command with correct syntax please? On Fri, Aug 14, 2015 at 10:44 AM, Naba nabajyoti.gosw...@gmail.com

Re: [gmx-users] g_sham

...@maillist.sys.kth.se on behalf of Naba nabajyoti.gosw...@gmail.com Sent: Friday, August 07, 2015 12:57 AM To: gromacs.org_gmx-users@maillist.sys.kth.se Subject: [gmx-users] g_sham Dear All, I searched a lot more things about g_sham in the mailing list and eventually getting confused

Re: [gmx-users] sample working DNA file?

Try using xleap of AmberTools. http://ambermd.org/tutorials/advanced/tutorial4/ On Wed, Aug 12, 2015 at 5:06 PM, Justin Lemkul jalem...@vt.edu wrote: On 8/12/15 6:07 AM, toannt wrote: Hi all, I have problems with a simple setup of DNA system. I try some programs to generate DNA pdb file.

Re: [gmx-users] g_sham

mail. Thanks a lot. On Thu, Aug 13, 2015 at 5:32 PM, Smith, Micholas D. smit...@ornl.gov wrote: Hi Naba, I believe you would want to do your second option if you want to include the contributions from all of the loops. If you are just interested in one loop, then you would do each seperately

[gmx-users] g_sham

time point for the corresponding minima obtained from g_sham? Thanks for all previous helps... Naba Bioinformatics Infrastructure Facility Department of Animal Biotechnology College of Veterinary Science Khanapara,Guwahati 781022 Assam, India -- Gromacs Users mailing list * Please search

[gmx-users] Regarding g_sham

time point for the corresponding minima obtained from g_sham? Thanks for all previous helps... Naba Nabajyoti Goswami Department of Animal Biotechnology College of Veterinary Science Assam Agricultural University Khanapara, Guwahati 781022 Assam, India -- Gromacs Users mailing list * Please

[gmx-users] Regarding g_sham

time point for the corresponding minima obtained from g_sham? Thanks for all previous helps... Naba Nabajyoti Goswami Department of Animal Biotechnology College of Veterinary Science Assam Agricultural University Khanapara, Guwahati 781022 Assam, India -- Gromacs Users mailing list * Please

Re: [gmx-users] ProDrg

How about ACPYPE for AMBER force field? On Tue, Dec 9, 2014 at 12:56 AM, Justin Lemkul jalem...@vt.edu wrote: On 12/8/14 2:12 PM, xy21hb wrote: Dear all, Since Justin mentioned in previous mails that PRODRG is almost unreliable, is there any reliable source for patching a new small