Hi, You're asking for a rotational fit, but you can't do that to a single atom. Fit e.g. to the protein, and then compute the SDF around the atom of interest.
Mark On Wed, Apr 4, 2018 at 6:08 AM Dilip H N <cy16f01.di...@nitk.edu.in> wrote: > I want to calculate water SDF around C-alpha of glycine molecule. So here i > have followed the commands.. > Step 2:- gmx trjconv -s nptmd.tpr -f nptmd.xtc -o abc.tng -boxcenter tric > -ur compact -pbc none > and it asks me > Select group for output > Group 0 ( System) has 1543 elements > Group 1 ( Protein) has 10 elements > Group 2 ( Protein-H) has 5 elements > Group 3 ( C-alpha) has 1 elements > Group 4 ( Backbone) has 3 elements > Group 5 ( MainChain) has 3 elements > Group 6 ( MainChain+Cb) has 3 elements > Group 7 ( MainChain+H) has 6 elements > Group 8 ( SideChain) has 4 elements > Group 9 ( SideChain-H) has 2 elements > Group 10 (Prot-Masses) has 10 elements > Group 11 (non-Protein) has 1533 elements > Group 12 ( Water) has 1533 elements > Group 13 ( SOL) has 1533 elements > Group 14 ( non-Water) has 10 elements > and i have selected Group 0 (System), > Step3:- gmx trjconv -s nptmd.tpr -f abc.tng -o def.tng -fit rot+trans > Select group for least squares fit Group 0 ( System) has 1543 elements > Group 1 ( Protein) has 10 elements Group 2 ( Protein-H) has 5 elements > Group 3 ( C-alpha) has 1 elements Group 4 ( Backbone) has 3 elements Group > 5 ( MainChain) has 3 elements Group 6 ( MainChain+Cb) has 3 elements Group > 7 ( MainChain+H) has 6 elements Group 8 ( SideChain) has 4 elements Group 9 > ( SideChain-H) has 2 elements Group 10 ( Prot-Masses) has 10 elements Group > 11 ( non-Protein) has 1533 elements Group 12 ( Water) has 1533 elements > Group 13 ( SOL) has 1533 elements Group 14 ( non-Water) has 10 elements > If i give group 3 (since it has C-alpha atoms), but i am getting an error > as > Fatal error: Need at least 2 atoms to fit! > > So, how can i solve this issue..?? since C-alpha is only one atom.. > > Thank you. > > > > <https://mailtrack.io/> Sent with Mailtrack > < > https://mailtrack.io?utm_source=gmail&utm_medium=signature&utm_campaign=signaturevirality&; > > > > On Tue, Apr 3, 2018 at 2:25 PM, Dilip H N <cy16f01.di...@nitk.edu.in> > wrote: > > > Hello, > > I want to do the Spatial Distribution Function, > > I tried to follow the manual gmx spatial..... > > I am following the five-step protocol which is given in gmx spatial > > manual.. > > 1) I have an index file ndx_CaOw.ndx (which contains the C-alpha and all > > the Ow's of water molecules, Is this index good or should i have all the > > molecules..??) > > 2) in the second step- "gmx trjconv -s a.tpr > > <http://manual.gromacs.org/online/tpr.html> -f a.tng > > <http://manual.gromacs.org/online/tng.html> -o b.tng > > <http://manual.gromacs.org/online/tng.html> -boxcenter tric -ur compact > > -pbc none" here we need to give the input file ie., -f a.tng from where > > does this .tng file i need to give the input..?? How do i create a .tng > > file.. what information does this tng file contain...?? > > > > Any suggestions... > > > > Thank you. > > -- > > With Best Regards, > > > > DILIP.H.N > > Ph.D Student > > > > <https://mailtrack.io/> Sent with Mailtrack > > < > https://mailtrack.io?utm_source=gmail&utm_medium=signature&utm_campaign=signaturevirality&; > > > > > > > > -- > With Best 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 > 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.
