Re: [gmx-users] Reference atoms for gmx mdmat and gmx rmsf

pecification is given for > RMSF calculation, i.e suppose only a protein group is specified. > > On Thu, 17 May 2018, 15:05 Joe Jordan, <e.jjorda...@gmail.com> wrote: > > > RMSF is calculated for the atoms or groups you specify in your selection > > string. If you say, e.g

Re: [gmx-users] Reference atoms for gmx mdmat and gmx rmsf

ead http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Joe Jordan -- Gromacs Users mailing list * Please search the ar

Re: [gmx-users] secondary structure analysis

gt; dssp.exe -i 5B1F2.PDB -o 1crn.dssp > error is > dssp.exe: command not found > thanking you > > On 5/16/18, Joe Jordan <e.jjorda...@gmail.com> wrote: > > Have you tried running the dssp command on a pdb file to ensure that it > is > > working as intended? FYI

Re: [gmx-users] secondary structure analysis

t; i have installed dssp2.04 in usr/local/bin. > > On 5/16/18, Joe Jordan <e.jjorda...@gmail.com> wrote: > > You have to point to where you have dssp installed. This may require you > to > > install dssp. > > > > On Wed, May 16, 2018 at 11:41 AM, SHAHEE ISLAM &l

Re: [gmx-users] secondary structure analysis

t; > * Please search the archive at http://www.gromacs.org/ > Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-user

Re: [gmx-users] trjconv ndec not working

_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Joe Jord

Re: [gmx-users] Regarding getting the coordinates within certain region of amino-acid

track.io?utm_source=gmail_medium=signature_campaign= > signaturevirality&> > > --- > With Best Regards, > > Dilip.H.N > PhD Student. > > On Thu, Apr 12, 2018 at 1:12 PM, Joe Jordan <e.jjorda...@gmail.com> wrote: > > > You need -on for gmx

Re: [gmx-users] Regarding getting the coordinates within certain region of amino-acid

lease search the archive at http://www.gromacs.org/ > > Support/Mailing_Lists/GMX-Users_List before posting! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)subscribe requests visit > > https://maillist.sys.kth.se/mailman/list

Re: [gmx-users] Regarding getting the coordinates within certain region of amino-acid

cribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Joe Jordan -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before

Re: [gmx-users] Protein atomic charges modeling question

sts > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Joe Jordan -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing

Re: [gmx-users] Perturbing Proteins

> > * Please search the archive at http://www.gromacs.org/ > Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-u

Re: [gmx-users] error in index file

<abhisek.m...@gmail.com> wrote: > I'm using v4.6.2 > > $make_ndx -f npt.gro > > > r 306 (residue num of ligand) > > name 24 Ligand > > This should do the work right ? > > On Tue, Apr 3, 2018 at 3:07 PM, Joe Jordan <e.jjorda...@gmail.com> wrote: > >

Re: [gmx-users] error in index file

folders/0B6O- > L5Y7BiGJfmQ4N2FpblBEcFNxaDZnaGpsUFFEUlotVWFjajR0UFFHNk5aYlhoSHVTWkU > > On Tue, Apr 3, 2018 at 2:53 PM, Joe Jordan <e.jjorda...@gmail.com> wrote: > > > Can you post the gro file and the resulting index file? > > > > On Tue, Apr 3, 2018 at

Re: [gmx-users] error in index file

t; *INDIA* > -- > Gromacs Users mailing list > > * Please search the archive at http://www.gromacs.org/ > Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https

Re: [gmx-users] Parameters in top

> > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Joe Jordan -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lis

Re: [gmx-users] RDF brads

Please search the archive at http://www.gromacs.org/ > Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.

Re: [gmx-users] Force displacement curve in SMD simulation

; * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Joe Jordan -- Gromacs Users mailing list * Please searc

Re: [gmx-users] Regarding time steps for calculation of Hydrogen Bond Dynamics

> > * Please search the archive at http://www.gromacs.org/ > Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_

Re: [gmx-users] source code for velocity information

s visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Joe Jordan -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posti

Re: [gmx-users] Structure factor and scattering intensity in gromacs 5.1.4

t > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Joe Jordan -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't p

Re: [gmx-users] rdf calculation for wormlike micelles

rch the archive at http://www.gromacs.org/ > Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or

Re: [gmx-users] Regarding calculation of Hydrogen-Bond

;> > > >> > > >> -- > > >> With Best Regards, > > >> > > >> DILIP.H.N > > >> Ph.D Student > > >> -- > > >> Gromacs Users mailing list > > >> > > >> * Please search the archive at http://www.

Re: [gmx-users] Sudden increase in RMSD values for 100ns simulation of protein-protein complex

g_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Joe Jordan -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/

Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 167, Issue 73

c > > than "Re: Contents of gromacs.org_gmx-users digest..." > > > > > > Today's Topics: > > > >1. rdf calculation for wormlike micelles (Esra Ka?ar) > >2. Re: rdf calculation for wormlike micelles (Joe Jordan) > > > > > > ---

Re: [gmx-users] rdf calculation for wormlike micelles

s/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. -- Joe Jordan -- Grom

Re: [gmx-users] GROMACS 5.1.4 and dssp 2.2.1

gt; > > send a mail to gmx-users-requ...@gromacs.org. > > > > > > > -- > > > Gromacs Users mailing list > > > > > > * Please search the archive at > > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > > posting

Re: [gmx-users] NPT equilibration failing at high temperature

Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Joe Jordan -- Groma

Re: [gmx-users] Simulation for Metalloprotein

list > > * Please search the archive at http://www.gromacs.org/ > Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-

Re: [gmx-users] About and index file of a monolayer...

ling_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Joe Jordan -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Maili

Re: [gmx-users] g_sans calculation

iling_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Joe Jorda