Re: [gmx-users] Can I get the fraction of solvent accessible surface area using "gmx sasa"?

I got it, Thank you very much for all the help! -- Original -- From: "ZHANG Cheng";<272699...@qq.com>; Date: Tue, Jan 16, 2018 08:46 PM To: "gromacs.org_gmx-users"; Subject: Re: Re: Re:Can I get the fraction

Re: [gmx-users] Can I get the fraction of solvent accessible surface area using "gmx sasa"?

On 1/16/18 7:46 AM, ZHANG Cheng wrote: Hi Justin, Thank you very much! The legend is "Total" for the command without -surface and -output. So I feel like if I do a division for the last columns from those two commands, I can just get the fraction of folded/unfolded? Strictly speaking,

Re: [gmx-users] Can I get the fraction of solvent accessible surface area using "gmx sasa"?

Hi Justin, Thank you very much! The legend is "Total" for the command without -surface and -output. So I feel like if I do a division for the last columns from those two commands, I can just get the fraction of folded/unfolded? e.g. 1.467/2.767 1.824/2.757 1.901/2.736 ... ...

Re: [gmx-users] Can I get the fraction of solvent accessible surface area using "gmx sasa"?

On 1/16/18 7:02 AM, ZHANG Cheng wrote: Hi Justin, Thank you very much. So I tried: gmx sasa -f md_0_1.xtc -s md_0_1.tpr -n index_C226S.ndx -o area.xvg -tu ns -surface 'group 0' -output 'group 1' And got: 0.000 206.8651.467 0.100 232.4501.824 0.200 225.984

Re: [gmx-users] Can I get the fraction of solvent accessible surface area using "gmx sasa"?

Hi Justin, Thank you very much. So I tried: gmx sasa -f md_0_1.xtc -s md_0_1.tpr -n index_C226S.ndx -o area.xvg -tu ns -surface 'group 0' -output 'group 1' And got: 0.000 206.8651.467 0.100 232.4501.824 0.200 225.9841.901 ... ... So my understanding

Re: [gmx-users] Can I get the fraction of solvent accessible surface area using "gmx sasa"?

On 1/16/18 6:19 AM, ZHANG Cheng wrote: Hi Alexandr, Thank you, but it is the same with spaces between | :( I provided the appropriate syntax before: http://manual.gromacs.org/documentation/2018-latest/user-guide/cmdline.html#g-sas -select and -output take strings that select what you want

Re: [gmx-users] Can I get the fraction of solvent accessible surface area using "gmx sasa"?

Hi Alexandr, Thank you, but it is the same with spaces between | :( Cheng -- Original -- From: "ZHANG Cheng";<272699...@qq.com>; Date: Tue, Jan 16, 2018 06:37 PM To: "gromacs.org_gmx-users"; Subject: Re:Re: Can

Re: [gmx-users] Can I get the fraction of solvent accessible surface area using "gmx sasa"?

On 16/01/2018 11:37, ZHANG Cheng wrote: Hi Justin, thank you very much. Sorry I still do not fully understand. I have an index file, in which the group 0 is all the residue atoms of the protein, group 1 is the first residue atoms. I want to calculate the sasa fraction of the residue 1. The

Re: [gmx-users] Can I get the fraction of solvent accessible surface area using "gmx sasa"?

Hi Justin, thank you very much. Sorry I still do not fully understand. I have an index file, in which the group 0 is all the residue atoms of the protein, group 1 is the first residue atoms. I want to calculate the sasa fraction of the residue 1. The fraction means: the sasa at folded state

Re: [gmx-users] Can I get the fraction of solvent accessible surface area using "gmx sasa"?

On 1/15/18 3:52 PM, ZHANG Cheng wrote: Thank you! So if I am using a index file, and the index 1 is the group I am interested, should I use the below? What is the difference between "-output" and "-o"? -output is the group you select for output, -o is the file to which the data are

Re: [gmx-users] Can I get the fraction of solvent accessible surface area using "gmx sasa"?

Thank you! So if I am using a index file, and the index 1 is the group I am interested, should I use the below? What is the difference between "-output" and "-o"? echo 1|gmx sasa -f md_0_1.xtc -s md_0_1.tpr -surface -output -n -o area.xvg -tu ns -- Original

Re: [gmx-users] Can I get the fraction of solvent accessible surface area using "gmx sasa"?

On 1/15/18 1:50 PM, ZHANG Cheng wrote: Dear Gromacs, This website can give us the Q(SASA), i.e. the fraction of SASA per residue, with values from 0 to 1. https://mathbio.crick.ac.uk/wiki/POPS Can I ask if we can use "gmx sasa" to obtain similar information? I do not like the "absolute"

[gmx-users] Can I get the fraction of solvent accessible surface area using "gmx sasa"?

Dear Gromacs, This website can give us the Q(SASA), i.e. the fraction of SASA per residue, with values from 0 to 1. https://mathbio.crick.ac.uk/wiki/POPS Can I ask if we can use "gmx sasa" to obtain similar information? I do not like the "absolute" sasa, as it could not reflect the relative