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

ification is given for > RMSF calculation, i.e suppose only a protein group is specified. > > On Thu, 17 May 2018, 15:05 Joe Jordan, wrote: > > > RMSF is calculated for the atoms or groups you specify in your selection > > string. If you say, e.g. "protein and name C

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

st? 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 search t

Re: [gmx-users] secondary structure analysis

.PDB -o 1crn.dssp > error is > dssp.exe: command not found > thanking you > > On 5/16/18, Joe Jordan wrote: > > Have you tried running the dssp command on a pdb file to ensure that it > is > > working as intended? FYI 4.5.5 is no longer supported so you may want to >

Re: [gmx-users] secondary structure analysis

usr/local/bin. > > On 5/16/18, Joe Jordan 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 > > wrote: > > > >> i want calculate the sec

Re: [gmx-users] secondary structure analysis

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 > send a mail to

Re: [gmx-users] trjconv ndec not working

osting! > > * 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 maili

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

472 0.957 1.477 1.030 > 388SOL OW 1169 1.307 1.001 1.370 > 388SOLHW1 1170 1.329 1.053 1.452 etc... > > Any suggestions are appreciated. > > Thank you. > ‌ > <https://mailtrack.io/> Sent with Mailtrack > <https://mailtrack.io?utm_source=gmail&a

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

/ > > 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 > > sen

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

sts 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

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

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_Lists/GMX-U

Re: [gmx-users] Perturbing Proteins

.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 > send a mail to gmx-u

Re: [gmx-users] error in index file

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 wrote: > > > I got a group with the right number of atoms

Re: [gmx-users] error in index file

s/0B6O- > L5Y7BiGJfmQ4N2FpblBEcFNxaDZnaGpsUFFEUlotVWFjajR0UFFHNk5aYlhoSHVTWkU > > On Tue, Apr 3, 2018 at 2:53 PM, Joe Jordan wrote: > > > Can you post the gro file and the resulting index file? > > > > On Tue, Apr 3, 2018 at 11:20 AM, abhisek Mondal > > wrote: > > > > >

Re: [gmx-users] error in index file

romacs 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://maillist.sys.kth.se

Re: [gmx-users] Parameters in top

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_Lists/GMX-Users_List before p

Re: [gmx-users] RDF brads

p://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 > send a mail to gmx-

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

ww.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 archive at h

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

ch 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 &g

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

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 post? Re

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

ribe 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] rdf calculation for wormlike micelles

w.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 > send a mail to gmx-

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

Regards, > > >> > > >> DILIP.H.N > > >> Ph.D Student > > >> -- > > >> Gromacs Users mailing list > > >> > > >> * Please search the archive at http://www.gromacs.org/ > > >> Support/Mailing_Lists/GMX-Users_List before

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

quests 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] gromacs.org_gmx-users Digest, Vol 167, Issue 73

t;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

> > * 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 * P

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

-requ...@gromacs.org. > > > > > > > -- > > > Gromacs Users mailing list > > > > > > * Please search the archive at > > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > > posting! > > > > > &g

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

ing! > > * 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 li

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

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

t/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 archive at http://www.gromacs.org/Support/

Re: [gmx-users] g_sans calculation

osting! > > * 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 m