Re: [gmx-users] Calculating the Hydrophobic and Hydrophilic SASA values on GROMACS version 5.1.2
Hi Supid, Got the point. Thanks a lot. On Wed, Sep 5, 2018 at 2:05 AM, Sudip Das wrote: > Hi Andrew, > Follow the below link. Hope that helps. > > http://www.gromacs.org/Documentation/How-tos/Tool_Changes_for_5.0 (follow > the 'g_sas' section) > > Regards, > Sudip > > On Wed, Sep 5, 2018 at 9:56 AM Andrew Srimalka Wijesekera < > 2014s14...@stu.cmb.ac.lk> wrote: > > > Dear all, > > > > I'm currently studying the structural changes and thermodynamic > properties > > of a protein structure when binding the ligand. Here I have ran the MD > run > > for 50 ns and calculate the SASA value from the gromacs 5.1.2 version. > > According to my knowledge I got only the total SASA value. But I want to > > get the hydrophobic and hydrophilic SASA values seperately from the > gromacs > > 5.1.2 version as well. Therefore would you please help me to solve this > > problem. > > Thanks in advance. > > -- > > 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://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > 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! > > * 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. > -- 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://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Calculating the Hydrophobic and Hydrophilic SASA values on GROMACS version 5.1.2
Hi Andrew, Follow the below link. Hope that helps. http://www.gromacs.org/Documentation/How-tos/Tool_Changes_for_5.0 (follow the 'g_sas' section) Regards, Sudip On Wed, Sep 5, 2018 at 9:56 AM Andrew Srimalka Wijesekera < 2014s14...@stu.cmb.ac.lk> wrote: > Dear all, > > I'm currently studying the structural changes and thermodynamic properties > of a protein structure when binding the ligand. Here I have ran the MD run > for 50 ns and calculate the SASA value from the gromacs 5.1.2 version. > According to my knowledge I got only the total SASA value. But I want to > get the hydrophobic and hydrophilic SASA values seperately from the gromacs > 5.1.2 version as well. Therefore would you please help me to solve this > problem. > Thanks in advance. > -- > 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://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > 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! * 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.
Re: [gmx-users] Calculating the Hydrophobic and Hydrophilic SASA values on GROMACS version 5.1.2
http://manual.gromacs.org/documentation/5.1-current/onlinehelp/gmx-sasa.html Appropriate use of index groups is what you need to do, separate out the hydrophobic and hydrophilic groups/atoms, then pass the index group via -n Catch ya, Dr. Dallas Warren Drug Delivery, Disposition and Dynamics Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3052 dallas.war...@monash.edu - When the only tool you own is a hammer, every problem begins to resemble a nail. On Wed, 5 Sep 2018 at 14:26, Andrew Srimalka Wijesekera <2014s14...@stu.cmb.ac.lk> wrote: > > Dear all, > > I'm currently studying the structural changes and thermodynamic properties > of a protein structure when binding the ligand. Here I have ran the MD run > for 50 ns and calculate the SASA value from the gromacs 5.1.2 version. > According to my knowledge I got only the total SASA value. But I want to > get the hydrophobic and hydrophilic SASA values seperately from the gromacs > 5.1.2 version as well. Therefore would you please help me to solve this > problem. > Thanks in advance. > -- > 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://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or 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! * 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.
[gmx-users] Calculating the Hydrophobic and Hydrophilic SASA values on GROMACS version 5.1.2
Dear all, I'm currently studying the structural changes and thermodynamic properties of a protein structure when binding the ligand. Here I have ran the MD run for 50 ns and calculate the SASA value from the gromacs 5.1.2 version. According to my knowledge I got only the total SASA value. But I want to get the hydrophobic and hydrophilic SASA values seperately from the gromacs 5.1.2 version as well. Therefore would you please help me to solve this problem. Thanks in advance. -- 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://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
