Re: Re: [gmx-users] how to make h-bond existence map?

Thanks to Florain for prompt reply May be this is trivial query to you I have done in this way 1. Making index file make_ndx -f .gro -o .ndx selected 7(mainchain+H)& r 24 26 45 67 78 the index showed like this [ MainChain+H_&_r_22_50_56_121_22 ] 370 370 371 371 372 372 386 386

Re: [gmx-users] how to make h-bond existence map?

Hi, On Wednesday, 3. September 2008, minnale wrote: > Thanks Florian for your detailed reply > when I mentioned -r and -a options in g_hbond command its showing > Fatal error: > Expected a real argument for option -a > similar error showing when I mentioned cutoff radius(-r) or cutoffangle > (-a)

Re: Re: [gmx-users] how to make h-bond existence map?

Thanks Florian for your detailed reply when I mentioned -r and -a options in g_hbond command its showing Fatal error: Expected a real argument for option -a similar error showing when I mentioned cutoff radius(-r) or cutoffangle (-a) Could you please suggest me Thanks in advance. On Wed, 03 Se

Re: [gmx-users] how to make h-bond existence map?

Hi, On Wednesday, 3. September 2008, minnale wrote: > Thanks Justin for your valuable suggestions > I have done the way you suggested. I gave command like this > g_hbond -f .xtc -s .tpr .ndx(contain 5 residues mainchain+H 25 atoms) -num > .xvg -hbm .xpm it showed > Select a group: 15 > Selected 1

Re: Re: [gmx-users] how to make h-bond existence map?

Thanks Justin for your valuable suggestions I have done the way you suggested. I gave command like this g_hbond -f .xtc -s .tpr .ndx(contain 5 residues mainchain+H 25 atoms) -num .xvg -hbm .xpm it showed Select a group: 15 Selected 15: 'MainChain+H_&_r_22_50_56_121_22' Select a group: 15 Sel

Re: [gmx-users] how to make h-bond existence map?

minnale wrote: Hi all, I am confusing while calculating hydrogen bonds of my protein.I issued this command g_hbond -f .xtc -s .tpr -num .xvg I didnt mention .ndx because I wanted to know the H-bonds in whole protein system. I have selected mainchain+H two times, command went fine and it s

[gmx-users] how to make h-bond existence map?

Hi all, I am confusing while calculating hydrogen bonds of my protein.I issued this command g_hbond -f .xtc -s .tpr -num .xvg I didnt mention .ndx because I wanted to know the H-bonds in whole protein system. I have selected mainchain+H two times, command went fine and it showed Select