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"<gromacs.org_gmx-users@maillist.sys.kth.se>;
Subject: Re:Re: 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 divided by the sasa when the residue is fully unfolded.
So as you said, "two selections, one for the surface, the other for what is
output".
) The manual says: "-surface should always consist of all non-solvent atoms in
the system", so in my case it should be group 0, right?
) The manual also says: "-output can specify additional selections, which
should be subsets of the calculation group", so in my case, it should be group
1, right?
so I tried:
echo 0 1|gmx sasa -f md_0_1.xtc -s md_0_1.tpr -n index_C226S.ndx -o area.xvg
-tu ns -surface -output
And got error message:
Error in user input:
Invalid selection '0 1 '
Near '1'
syntax error
I also tried "echo 1 0", and got the similar error:
Error in user input:
Invalid selection '1 0 '
Near '0'
syntax error
Can you please help me? Thank you very much!
------------------ Original ------------------
From: "ZHANG Cheng";<272699...@qq.com>;
Date: Tue, Jan 16, 2018 04:52 AM
To: "gromacs.org_gmx-users"<gromacs.org_gmx-users@maillist.sys.kth.se>;
Subject: Re: 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 ------------------
From: "ZHANG Cheng";<272699...@qq.com>;
Date: Tue, Jan 16, 2018 02:50 AM
To: "gromacs.org_gmx-users"<gromacs.org_gmx-users@maillist.sys.kth.se>;
Subject: 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 exposure extent of a
residue. For example, a buried big residue may have similar sasa as an exposed
small residue.
Thank you.
Yours sincerely
Cheng
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