Re: [gmx-users] Glycosylation of ASN

Hi, Have you tried reducing the timestep in mdp? On Mon, May 4, 2020, 2:52 AM Naba wrote: > Dear users and developers, > > I have spent extensive amount of time to model glycosylated ASN residues > covalently linked with N-ACETYL-D-GLUCOSAMINE (NAG) in a glycoprotein using > Amber99SB-ILDN

Re: [gmx-users] how to generate average structure from trajectory

Hi, For discarding first 1ns , modify the trajectory with *trjconv* with *-b* flag. Use the modified trajectory for cluster analysis with *gmx cluster* to get an average structure from a highly populated cluster. Thanks & Regards, -- *Subhomoi Borkotoky, Ph. D.* Ku

Re: [gmx-users] Listing residues in gromacs

with the index file from gmx select, but not successful. Thanks & Regards, -- *Subhomoi Borkotoky, Ph. D.* Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, New Delhi-110016, India. Alternate E-mail : subho...@yahoo.com On Tue, Feb 18,

[gmx-users] Listing residues in gromacs

Hi, Is there any option in gromacs to list residues/atoms around a reference group? I have checked trjorder , but it only gives number of molecules. Thanks & Regards, -- *Subhomoi Borkotoky, Ph. D.* Kusuma School of Biological Sciences, Indian Institute of Techno

[gmx-users] Listing residues in gromacs

Hi, Is there any option in gromacs to list residues/atoms around a reference group? I have checked trjorder , but it only gives number of molecules. Thanks & Regards, -- *Subhomoi Borkotoky, Ph. D.* Kusuma School of Biological Sciences, Indian Institute of Techno

Re: [gmx-users] Distance Calculation peptide-membrane

Hi, Please find the following link. https://drive.google.com/open?id=0BzFTh9SCRtetd0Eta21XR2hIY0hvZDRqLW9UemRfUl81Q0pz Thanks & Regards, -- *Subhomoi B* On Thu, Dec 26, 2019 at 6:56 PM Justin Lemkul wrote: > > > On 12/26/19 11:34 AM, Subhomoi Borkotoky

[gmx-users] Distance Calculation peptide-membrane

Hi, I am running a peptide-membrane analysis, where I want to check the distance between peptide and membrane over time (between center of mass). However, I am getting a graph like one pasted below even after pbc correction. Kindly suggest a possible solution. [image: image.png] Thanks &

Re: [gmx-users] how to calculate average structure

my aptamer > without ligand, I need to check different interaction between aptamer > and ligand during simulation time.It would be pleasure if you have any > suggestion. > > Thanks a lot > > Maryam > > On 2019-10-05 08:43, Subhomoi Borkotoky wrote: > > > Hi,

Re: [gmx-users] how to calculate average structure

Hi, You can use "gmx cluster" to get an average structure based on RMSD. Just use an appropriate cut-off. Regards, Subhomoi B. On Sat, Oct 5, 2019, 10:01 AM mmousivand93 wrote: > Dear all; > > I performed a molecular dynamic simulation(50ns) for a complex > aptamer-ligand and I am going to

Re: [gmx-users] Using grace in windows

Hi, You can use qtGrace in Windows directly. Regards, Subhomoi B. On Wed, May 8, 2019, 7:14 PM DEEPANSHU SINGLA wrote: > I am trying to plot graph from gromacs generated xvg files in windows 10 > using Linux subsystem command line. I installed grace using the same > command line. When I try

Re: [gmx-users] ramachandran plot

Hi Javed, I hope *gmx rama* will solve the issue. http://manual.gromacs.org/archive/5.0.4/programs/gmx-rama.html Thanks & Regards, -- *Subhomoi Borkotoky, Ph. D.* DBT Research Associate, Kusuma School of Biological Sciences, Indian Institute of Technology Delhi,

Re: [gmx-users] Secondary structure propensity.

Thanks for the addition. On 16 Feb 2018 6:22 pm, "Justin Lemkul" <jalem...@vt.edu> wrote: > > > On 2/16/18 3:40 AM, Subhomoi Borkotoky wrote: > >> Hello, >> >> I believe *do_dssp* will do the trick. Generate the *.xpm* matrix file , >>

Re: [gmx-users] Secondary structure propensity.

s visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Yours Sincerely, -- *Dr. Subhomoi Borkotoky, Ph. D.* DBT Research Associate, Kusuma School of Biological Sciences, Indian I

Re: [gmx-users] how to generate a trr file

Hi, You can use "trjconv" command and specify "-e 5". Hope it helps!! Regards, Subhomoi B. On 17 Sep 2017 8:34 pm, "marzieh dehghan" wrote: > Dear all > Hi > > I performed molecular dynamics simulation during 100 ns, but now I want to > create a trr or xtc

Re: [gmx-users] Gromacs enquiry

ailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Yours Sincerely, -- SUBHOMOI BORKOTOKY, Centre for Bioinformatics Pondicherry University Pondicherry,INDIA. Alternate Email: subho...@bicpu.edu.in <subho...@mails.bicpu.edu.i

[gmx-users] Regarding sampling convergence

them to compare? -- Yours Sincerely, -- SUBHOMOI BORKOTOKY, Centre for Bioinformatics Pondicherry University Pondicherry,INDIA. Alternate Email: subho...@mails.bicpu.edu.in https://scholar.google.co.in/citations?user=bJz7GokJ=en -- Gromacs Users mailing list

[gmx-users] sampling convergence of FEL

halves to compare? -- Yours Sincerely, -- SUBHOMOI BORKOTOKY, Centre for Bioinformatics Pondicherry University Pondicherry,INDIA. Alternate Email: subho...@mails.bicpu.edu.in https://scholar.google.co.in/citations?user=bJz7GokJ=en -- Gromacs Users mailing list * Please

Re: [gmx-users] Number of H bonds formed between ligand and amino acid residues

man/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Yours Sincerely, -- SUBHOMOI BORKOTOKY, Centre for Bioinformatics Pondicherry University Pondicherry,INDIA. Alternate Email: subho...@mails.bicpu.edu.in -- Gromacs Users mailin

[gmx-users] Regarding Gromacs compatibilty

Hello, I would like to know whether it is possible extend a simulation ran with gromacs 4.6 in gromacs 5. If it is possible, what is the procedure? -- Thanks and Regards, -- SUBHOMOI BORKOTOKY, Centre for Bioinformatics Pondicherry University Pondicherry,INDIA