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

2018-01-16 Thread ZHANG Cheng 
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 "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
... ...


-- Original --
From:  "ZHANG Cheng";<272699...@qq.com>;
Date:  Tue, Jan 16, 2018 08:02 PM
To:  "gromacs.org_gmx-users";

Subject:  Re: Re: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 is
) 1st column is the time
) 2nd column is the sasa of the whole protein
) 3rd column is the sasa of the particular group
Thank you for that.


But may I ask
1) if it is possible to calculate the fraction for a particular group in this 
way:
(sasa of the state in the xtc file)/(sasa when that group is fully unfolded)
Because a big buried residue may have similar sasa compared to a small exposed 
residue, so the "absolute" sasa of each residue could not reflect their buried 
extents individually.


2) When I do not use -surface and -output, but use echo:
echo 1|gmx sasa -f md_0_1.xtc -s md_0_1.tpr -n index_C226S.ndx -o area.xvg -tu 
ns


I got:
  0.0002.767
  0.1002.757
  0.2002.736

  ... ...


Do you know what is the meaning of the second column?


Thank you!




-- Original --
From:  "ZHANG Cheng";<272699...@qq.com>;
Date:  Tue, Jan 16, 2018 07:19 PM
To:  "gromacs.org_gmx-users";

Subject:  Re:   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 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";

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";

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.

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

2018-01-16 Thread Justin Lemkul 



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, because you have artificial edges of that residue 
created by ignoring the fact that there are always residues flanking it. 
And you also have no guarantee that even in an "unfolded" state that 
this residue is 100% exposed to solvent. As an approximation, sure, but 
there is some level of error that may range from negligible to 
considerable, depending entirely upon the unfolded ensemble.


-Justin



e.g.
1.467/2.767
1.824/2.757
1.901/2.736
... ...


-- Original --
From:  "ZHANG Cheng";<272699...@qq.com>;
Date:  Tue, Jan 16, 2018 08:02 PM
To:  "gromacs.org_gmx-users";

Subject:  Re: Re: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 is
) 1st column is the time
) 2nd column is the sasa of the whole protein
) 3rd column is the sasa of the particular group
Thank you for that.


But may I ask
1) if it is possible to calculate the fraction for a particular group in this 
way:
(sasa of the state in the xtc file)/(sasa when that group is fully unfolded)
Because a big buried residue may have similar sasa compared to a small exposed residue, 
so the "absolute" sasa of each residue could not reflect their buried extents 
individually.


2) When I do not use -surface and -output, but use echo:
echo 1|gmx sasa -f md_0_1.xtc -s md_0_1.tpr -n index_C226S.ndx -o area.xvg -tu 
ns


I got:
   0.0002.767
   0.1002.757
   0.2002.736

   ... ...


Do you know what is the meaning of the second column?


Thank you!




-- Original --
From:  "ZHANG Cheng";<272699...@qq.com>;
Date:  Tue, Jan 16, 2018 07:19 PM
To:  "gromacs.org_gmx-users";

Subject:  Re:   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 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";

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";

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

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

2018-01-16 Thread ZHANG Cheng 
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
... ...


-- Original --
From:  "ZHANG Cheng";<272699...@qq.com>;
Date:  Tue, Jan 16, 2018 08:02 PM
To:  "gromacs.org_gmx-users";

Subject:  Re: Re: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 is
) 1st column is the time
) 2nd column is the sasa of the whole protein
) 3rd column is the sasa of the particular group
Thank you for that.


But may I ask
1) if it is possible to calculate the fraction for a particular group in this 
way:
(sasa of the state in the xtc file)/(sasa when that group is fully unfolded)
Because a big buried residue may have similar sasa compared to a small exposed 
residue, so the "absolute" sasa of each residue could not reflect their buried 
extents individually.


2) When I do not use -surface and -output, but use echo:
echo 1|gmx sasa -f md_0_1.xtc -s md_0_1.tpr -n index_C226S.ndx -o area.xvg -tu 
ns


I got:
  0.0002.767
  0.1002.757
  0.2002.736

  ... ...


Do you know what is the meaning of the second column?


Thank you!




-- Original --
From:  "ZHANG Cheng";<272699...@qq.com>;
Date:  Tue, Jan 16, 2018 07:19 PM
To:  "gromacs.org_gmx-users";

Subject:  Re:   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 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";

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";

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
-- 
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

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

2018-01-16 Thread Justin Lemkul 



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  225.9841.901

   ... ...


So my understanding is
) 1st column is the time
) 2nd column is the sasa of the whole protein
) 3rd column is the sasa of the particular group
Thank you for that.


But may I ask
1) if it is possible to calculate the fraction for a particular group in this 
way:
(sasa of the state in the xtc file)/(sasa when that group is fully unfolded)
Because a big buried residue may have similar sasa compared to a small exposed residue, 
so the "absolute" sasa of each residue could not reflect their buried extents 
individually.


gmx sasa will compute the SASA of the chosen atoms in the supplied 
configuration(s). If you want to do further manipulations, you'll have 
to script that yourself as a post-processing task.




2) When I do not use -surface and -output, but use echo:
echo 1|gmx sasa -f md_0_1.xtc -s md_0_1.tpr -n index_C226S.ndx -o area.xvg -tu 
ns


I got:
   0.0002.767
   0.1002.757
   0.2002.736

   ... ...


Do you know what is the meaning of the second column?


It should be labeled in the header of the output file, but it's the SASA 
of the chosen group of atoms, in this instance assuming that the entire 
group is solvent-exposed (because you're not computing a full surface 
here, just the SASA of the chosen atoms).


-Justin

--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

==

--
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* 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

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mail to gmx-users-requ...@gromacs.org.

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

2018-01-16 Thread ZHANG Cheng 
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
) 1st column is the time
) 2nd column is the sasa of the whole protein
) 3rd column is the sasa of the particular group
Thank you for that.


But may I ask
1) if it is possible to calculate the fraction for a particular group in this 
way:
(sasa of the state in the xtc file)/(sasa when that group is fully unfolded)
Because a big buried residue may have similar sasa compared to a small exposed 
residue, so the "absolute" sasa of each residue could not reflect their buried 
extents individually.


2) When I do not use -surface and -output, but use echo:
echo 1|gmx sasa -f md_0_1.xtc -s md_0_1.tpr -n index_C226S.ndx -o area.xvg -tu 
ns


I got:
  0.0002.767
  0.1002.757
  0.2002.736

  ... ...


Do you know what is the meaning of the second column?


Thank you!




-- Original --
From:  "ZHANG Cheng";<272699...@qq.com>;
Date:  Tue, Jan 16, 2018 07:19 PM
To:  "gromacs.org_gmx-users";

Subject:  Re:   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 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";

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";

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
-- 
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.

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

2018-01-16 Thread Justin Lemkul 



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 for each. Do 
that, not echo.


-Justin



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 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";

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";

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


--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

==

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

2018-01-16 Thread ZHANG Cheng 
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 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";

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";

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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http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

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

2018-01-16 Thread Alexandr Nasedkin 

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 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


Try to place spaces between '|' and other arguments:
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 see if it works.



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";

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";

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

-Alexandr

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mail to gmx-users-requ...@gromacs.org.

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

2018-01-16 Thread ZHANG Cheng 
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";

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";

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
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

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

2018-01-15 Thread Justin Lemkul 



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. Please read gmx help sasa if you're not clear what the 
options are doing.




echo 1|gmx sasa -f md_0_1.xtc -s md_0_1.tpr -surface -output -n -o area.xvg -tu 
ns


The command requires two selections, one for the surface, the other for 
what is output. See 
http://manual.gromacs.org/documentation/2018-latest/user-guide/cmdline.html#g-sas


-Justin

--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

==

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

2018-01-15 Thread ZHANG Cheng 
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";

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
-- 
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

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

2018-01-15 Thread Justin Lemkul 



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" 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.


Yes, if you select the full surface as the calculation group and the 
residue(s) of interest as the output group, you can easily calculate the 
relative contribution to the surface.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

==

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