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 of solvent accessible surface
area using "g
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, no,
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
... ...
-
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
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 is
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 f
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 I get the fraction of solvent accessible su
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 f
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 di
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 written.
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
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" sas
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 exp
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