subject:"\[gmx\-users\] g

[gmx-users] g_sas on pdb files

2013-06-18 Thread erin.cutts

I'm trying to compare the hydrophobic surface generated from my trajectory
with g_sas to a range of random coil .pdb files with my protein sequence,
but I can't figure out how to make the structure+mass input that is required
for g_sas from my pdb files i.e. in the manual
Structure+mass(db): tpr tpb tpa gro g96 pdb
Just using the pdb file itself results in it not being able to define which
residues are hydrophobic and it doesn't work. I want the two calculations to
be as comparable as possible.

Thanks for any help people can give.

Erin



--
View this message in context: 
http://gromacs.5086.x6.nabble.com/g-sas-on-pdb-files-tp5009248.html
Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] g_sas on pdb files

2013-06-18 Thread Justin Lemkul




On 6/18/13 7:41 AM, erin.cutts wrote:

I'm trying to compare the hydrophobic surface generated from my trajectory
with g_sas to a range of random coil .pdb files with my protein sequence,
but I can't figure out how to make the structure+mass input that is required
for g_sas from my pdb files i.e. in the manual
Structure+mass(db): tpr tpb tpa gro g96 pdb
Just using the pdb file itself results in it not being able to define which
residues are hydrophobic and it doesn't work. I want the two calculations to
be as comparable as possible.

Thanks for any help people can give.


Within g_sas, hydrophobicity is defined by the charge carried by each atom, and 
thus a .tpr file is required.  While not strictly necessary, I think it makes 
the result more reliable.  Otherwise, I believe g_sas defaults to guessing based 
on atom names.  For comparison purposes, that may work, but in terms of absolute 
figures, it may not be reliable.


-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] g_sas : Total surface area

2012-12-12 Thread Mark Abraham

On Wed, Dec 12, 2012 at 9:06 AM, Kavyashree M hmkv...@gmail.com wrote:

 Dear users,

 I was calculating solvent accessible surface area for a trajectory
 using g_sas. I used an index file with 3 sets (A, B, C) of mutually
 exclusive residues but summing up to 20 amino acids. Then using
 g_sas calculated sas for these 3 sets separately and whole protein
 separately for the same trajectory.
 I was expecting that the average value of
 Total surface area (protein) ~ Total surface area (A)+Total surface area
 (B)+Total surface area (C)
 But it is not so.
 Could anyone explain me why?


Not without seeing any numbers. You're probably thinking that the surface
area of A excludes the interfacial area to the other sets, but it doesn't.

Mark
-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] g_sas : Total surface area

2012-12-12 Thread francesco oteri

Hi Kavya,
Can you better describe your system?
As Mark suggested, could you supply some number?

Francesco


2012/12/12 Mark Abraham mark.j.abra...@gmail.com

 On Wed, Dec 12, 2012 at 9:06 AM, Kavyashree M hmkv...@gmail.com wrote:

  Dear users,
 
  I was calculating solvent accessible surface area for a trajectory
  using g_sas. I used an index file with 3 sets (A, B, C) of mutually
  exclusive residues but summing up to 20 amino acids. Then using
  g_sas calculated sas for these 3 sets separately and whole protein
  separately for the same trajectory.
  I was expecting that the average value of
  Total surface area (protein) ~ Total surface area (A)+Total surface area
  (B)+Total surface area (C)
  But it is not so.
  Could anyone explain me why?
 

 Not without seeing any numbers. You're probably thinking that the surface
 area of A excludes the interfacial area to the other sets, but it doesn't.

 Mark
 --
 gmx-users mailing listgmx-users@gromacs.org
 http://lists.gromacs.org/mailman/listinfo/gmx-users
 * Please search the archive at
 http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
 * Please don't post (un)subscribe requests to the list. Use the
 www interface or send it to gmx-users-requ...@gromacs.org.
 * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists




-- 
Cordiali saluti, Dr.Oteri Francesco
-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] g_sas : Total surface area

2012-12-12 Thread Kavyashree M

Thank you very much for your replies.

The system consists of a homodimer in tip4p dodecahedron box
simulated using OPLSAA ff.

The A B C here are the amino acids:
A- S T N Q G P H
B- A V L I M C F Y W
C- D E K R

So these are set in an index file and i used each one of these
to calculate sasa in g_sas.
When the g_sas calculation starts it specifies the number of
hydrophobic atoms, one of the example -
For the whole protein -
4644 out of 7590 atoms were classified as hydrophobic
For group A of same protein -
702 out of 1424 atoms were classified as hydrophobic
For group B of same protein -
2614 out of 3496 atoms were classified as hydrophobic
For group C of same protein -
1328 out of 2670 atoms were classified as hydrophobic

In this the number of hydrophobic atoms of A, B and C adds
up to the total hydrophobic atoms in whole protein.

but after the calculation is over the average values of Total sas
(legend S2 of area.xvg file) of the protein and Total sas of A, B
and C are given below
Whole protein - 254.04nm^(-2)
A - 175.87nm^(-2)
B - 211.33nm^(-2)
C - 264.65nm^(-2)

I expected that the average total sas of Whole protein atleast approximately
equal the sum of Total sas of A, B and C. If not why? All calculations are
done for the same trajectory after equilibrating.

Thank you
Kavya



On Wed, Dec 12, 2012 at 5:20 PM, francesco oteri
francesco.ot...@gmail.comwrote:

 Hi Kavya,
 Can you better describe your system?
 As Mark suggested, could you supply some number?

 Francesco


 2012/12/12 Mark Abraham mark.j.abra...@gmail.com

  On Wed, Dec 12, 2012 at 9:06 AM, Kavyashree M hmkv...@gmail.com wrote:
 
   Dear users,
  
   I was calculating solvent accessible surface area for a trajectory
   using g_sas. I used an index file with 3 sets (A, B, C) of mutually
   exclusive residues but summing up to 20 amino acids. Then using
   g_sas calculated sas for these 3 sets separately and whole protein
   separately for the same trajectory.
   I was expecting that the average value of
   Total surface area (protein) ~ Total surface area (A)+Total surface
 area
   (B)+Total surface area (C)
   But it is not so.
   Could anyone explain me why?
  
 
  Not without seeing any numbers. You're probably thinking that the surface
  area of A excludes the interfacial area to the other sets, but it
 doesn't.
 
  Mark
  --
  gmx-users mailing listgmx-users@gromacs.org
  http://lists.gromacs.org/mailman/listinfo/gmx-users
  * Please search the archive at
  http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
  * Please don't post (un)subscribe requests to the list. Use the
  www interface or send it to gmx-users-requ...@gromacs.org.
  * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
 



 --
 Cordiali saluti, Dr.Oteri Francesco
 --
 gmx-users mailing listgmx-users@gromacs.org
 http://lists.gromacs.org/mailman/listinfo/gmx-users
 * Please search the archive at
 http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
 * Please don't post (un)subscribe requests to the list. Use the
 www interface or send it to gmx-users-requ...@gromacs.org.
 * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] g_sas : Total surface area

2012-12-12 Thread Justin Lemkul




On 12/12/12 9:37 AM, Kavyashree M wrote:

Thank you very much for your replies.

The system consists of a homodimer in tip4p dodecahedron box
simulated using OPLSAA ff.

The A B C here are the amino acids:
A- S T N Q G P H
B- A V L I M C F Y W
C- D E K R

So these are set in an index file and i used each one of these
to calculate sasa in g_sas.
When the g_sas calculation starts it specifies the number of
hydrophobic atoms, one of the example -
For the whole protein -
4644 out of 7590 atoms were classified as hydrophobic
For group A of same protein -
702 out of 1424 atoms were classified as hydrophobic
For group B of same protein -
2614 out of 3496 atoms were classified as hydrophobic
For group C of same protein -
1328 out of 2670 atoms were classified as hydrophobic

In this the number of hydrophobic atoms of A, B and C adds
up to the total hydrophobic atoms in whole protein.

but after the calculation is over the average values of Total sas
(legend S2 of area.xvg file) of the protein and Total sas of A, B
and C are given below
Whole protein - 254.04nm^(-2)
A - 175.87nm^(-2)
B - 211.33nm^(-2)
C - 264.65nm^(-2)

I expected that the average total sas of Whole protein atleast approximately
equal the sum of Total sas of A, B and C. If not why? All calculations are
done for the same trajectory after equilibrating.



Are you selecting the correct groups when running g_sas?  For instance, you 
should be selecting Protein for the surface calculation, and then your custom 
subsets for output.  If you use the subsets for both surface calculation and 
output, you will get an artificially inflated value that includes extra surface 
area that is actually buried in the context of the whole structure.


-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] g_sas : Total surface area

2012-12-12 Thread Kavyashree M

Sir,

Oh! I was using sunset index numbers for both. I am sorry. I will try
that and see. First option as protein and next the subset. Thank you
very much.

Kavya

On Wed, Dec 12, 2012 at 8:16 PM, Justin Lemkul jalem...@vt.edu wrote:

On 12/12/12 9:37 AM, Kavyashree M wrote:

Thank you very much for your replies.

The system consists of a homodimer in tip4p dodecahedron box
simulated using OPLSAA ff.

The A B C here are the amino acids:
A- S T N Q G P H
B- A V L I M C F Y W
C- D E K R

So these are set in an index file and i used each one of these
to calculate sasa in g_sas.
When the g_sas calculation starts it specifies the number of
hydrophobic atoms, one of the example -
For the whole protein -
4644 out of 7590 atoms were classified as hydrophobic
For group A of same protein -
702 out of 1424 atoms were classified as hydrophobic
For group B of same protein -
2614 out of 3496 atoms were classified as hydrophobic
For group C of same protein -
1328 out of 2670 atoms were classified as hydrophobic

In this the number of hydrophobic atoms of A, B and C adds
up to the total hydrophobic atoms in whole protein.

but after the calculation is over the average values of Total sas
(legend S2 of area.xvg file) of the protein and Total sas of A, B
and C are given below
Whole protein - 254.04nm^(-2)
A - 175.87nm^(-2)
B - 211.33nm^(-2)
C - 264.65nm^(-2)

I expected that the average total sas of Whole protein atleast
approximately
equal the sum of Total sas of A, B and C. If not why? All calculations are
done for the same trajectory after equilibrating.

Are you selecting the correct groups when running g_sas? For instance,
you should be selecting Protein for the surface calculation, and then
your custom subsets for output. If you use the subsets for both surface
calculation and output, you will get an artificially inflated value that
includes extra surface area that is actually buried in the context of the
whole structure.

-Justin

--
==**==

Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

==**==

--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at http://www.gromacs.org/**
Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore
posting!
* Please don't post (un)subscribe requests to the list. Use the www
interface or send it to gmx-users-requ...@gromacs.org.
* Can't post? Read
http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists

--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] g_sas : Total surface area

2012-12-12 Thread Kavyashree M

I meant subset :)

On Wed, Dec 12, 2012 at 8:21 PM, Kavyashree M hmkv...@gmail.com wrote:

Sir,

Oh! I was using sunset index numbers for both. I am sorry. I will try
that and see. First option as protein and next the subset. Thank you
very much.

Kavya

On Wed, Dec 12, 2012 at 8:16 PM, Justin Lemkul jalem...@vt.edu wrote:

On 12/12/12 9:37 AM, Kavyashree M wrote:

Thank you very much for your replies.

The system consists of a homodimer in tip4p dodecahedron box
simulated using OPLSAA ff.

The A B C here are the amino acids:
A- S T N Q G P H
B- A V L I M C F Y W
C- D E K R

In this the number of hydrophobic atoms of A, B and C adds
up to the total hydrophobic atoms in whole protein.

I expected that the average total sas of Whole protein atleast
approximately
equal the sum of Total sas of A, B and C. If not why? All calculations
are
done for the same trajectory after equilibrating.

-Justin

--
==**==

==**==

Re: [gmx-users] G_sas change in hydrophilic and hydrophobic surface area

2012-11-22 Thread Justin Lemkul




On 11/22/12 2:36 AM, rama david wrote:

Dear user ,
I simulate the two  protein in random coil position, when they come close
they form antiparallel  beta sheet structure.
I want to calculate the change in hydrophilic and hydrophobic surface
area over my simulation time.
For usig g_sas  Should I have to make the different index group for
hydrophilic and hydrophobic residues
Or should only have to select the option protein both the time.



The whole protein should always be the group for the surface calculation. 
Whatever subset of those atoms (i.e. residues of interest) can be the output group.


-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] G_sas change in hydrophilic and hydrophobic surface area

2012-11-22 Thread rama david

Hi justin,
Thank you for reply.
As per your suggestion,
The whole protein should always be the group for the
surface calculation. Whatever subset of those atoms (i.e. residues of
interest) can be the output group.

So as per your suggestion I have to select the protein as my option 1 and
for output I have to select the hydrophilic residues or hydrophobic
residues as per my choice Is these is right ??? or Am I wrong???
( That means I have to make to index file that contain two groups
hydrophilic and hydrophobic residues.)

Would you please tell me why not select the protein as output, as I am
calculating the change in the hydrophilic and hydrophobic surface area of
protein...???

As per the manual,

The program will ask for a group for the surface calculation and a
group for the output. The
calculation group should always consists of all the non-solvent atoms in the
system. The output group can be the whole or part of the calculation group.

As two protein comes closer in simulation they formed the antiparrallel
beta strand, I want to find the change in hydrophilic and hydrophobic
surface area of protein...

With Best Wishes and Regards,
Rama david

On Thu, Nov 22, 2012 at 11:32 PM, Justin Lemkul jalem...@vt.edu wrote:

On 11/22/12 2:36 AM, rama david wrote:

Dear user ,
I simulate the two protein in random coil position, when they come close
they form antiparallel beta sheet structure.
I want to calculate the change in hydrophilic and hydrophobic surface
area over my simulation time.
For usig g_sas Should I have to make the different index group for
hydrophilic and hydrophobic residues
Or should only have to select the option protein both the time.

The whole protein should always be the group for the surface calculation.
Whatever subset of those atoms (i.e. residues of interest) can be the
output group.

-Justin

--
==**==

==**==
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at http://www.gromacs.org/**
Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore
posting!
* Please don't post (un)subscribe requests to the list. Use the www
interface or send it to gmx-users-requ...@gromacs.org.
* Can't post? Read
http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] G_sas change in hydrophilic and hydrophobic surface area

2012-11-22 Thread Justin Lemkul

On 11/22/12 1:54 PM, rama david wrote:

Would you please tell me why not select the protein as output, as I am
calculating the change in the hydrophilic and hydrophobic surface area of
protein...???

You can certainly do that. Perhaps I misunderstood the original post. I
thought you were curious about the solvent exposure of certain residues. If you
only care about the evolution of total polar and nonpolar surface areas, then
choose Protein for both groups.

-Justin

As per the manual,

As two protein comes closer in simulation they formed the antiparrallel
beta strand, I want to find the change in hydrophilic and hydrophobic
surface area of protein...

With Best Wishes and Regards,
Rama david

On Thu, Nov 22, 2012 at 11:32 PM, Justin Lemkul jalem...@vt.edu wrote:

On 11/22/12 2:36 AM, rama david wrote:

The whole protein should always be the group for the surface calculation.
Whatever subset of those atoms (i.e. residues of interest) can be the
output group.

-Justin

--
==**==

Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] G_sas change in hydrophilic and hydrophobic surface area

2012-11-22 Thread rama david

Thank you justin

With best wishes and regards,
Rama David

On Fri, Nov 23, 2012 at 12:45 AM, Justin Lemkul jalem...@vt.edu wrote:

On 11/22/12 1:54 PM, rama david wrote:

Would you please tell me why not select the protein as output, as I am
calculating the change in the hydrophilic and hydrophobic surface area of
protein...???

You can certainly do that. Perhaps I misunderstood the original post. I
thought you were curious about the solvent exposure of certain residues.
If you only care about the evolution of total polar and nonpolar surface
areas, then choose Protein for both groups.

-Justin

As per the manual,

The program will ask for a group for the surface calculation and a
group for the output. The
calculation group should always consists of all the non-solvent atoms in
the
system. The output group can be the whole or part of the calculation
group.

As two protein comes closer in simulation they formed the antiparrallel
beta strand, I want to find the change in hydrophilic and hydrophobic
surface area of protein...

With Best Wishes and Regards,
Rama david

On Thu, Nov 22, 2012 at 11:32 PM, Justin Lemkul jalem...@vt.edu wrote:

On 11/22/12 2:36 AM, rama david wrote:

Dear user ,
I simulate the two protein in random coil position, when they come
close
they form antiparallel beta sheet structure.
I want to calculate the change in hydrophilic and hydrophobic
surface
area over my simulation time.
For usig g_sas Should I have to make the different index group for
hydrophilic and hydrophobic residues
Or should only have to select the option protein both the time.

The whole protein should always be the group for the surface
calculation.
Whatever subset of those atoms (i.e. residues of interest) can be the
output group.

-Justin

--
====

Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justinhttp://vt.edu/Pages/Personal/justin
h**ttp://www.bevanlab.biochem.vt.**edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

====

--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-usershttp://lists.gromacs.org/**mailman/listinfo/gmx-users
htt**p://lists.gromacs.org/mailman/**listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users

* Please search the archive at http://www.gromacs.org/**
Support/Mailing_Lists/Searchh**ttp://www.gromacs.org/Support/**
Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore
posting!

* Please don't post (un)subscribe requests to the list. Use the www
interface or send it to gmx-users-requ...@gromacs.org.
* Can't post? Read
http://www.gromacs.org/Support/Mailing_Listshttp://www.gromacs.org/**Support/Mailing_Lists
http://**www.gromacs.org/Support/**Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists

--
==**==

[gmx-users] g_sas doubt -reg

2012-09-02 Thread venkatesh s

Dear Sir / Madam,
 I want run Solvent accessible surface area in
gromacs,i aware about  g_sas is there but for selecting group little bit
confusing

Reading frame   0 time0.000   Select a group for calculation of
surface and a group for output:
Group 0 ( System) has 210538 elements
Group 1 (Protein) has  1517 elements
Group 2 (  Protein-H) has  1199 elements
Group 3 (C-alpha) has   158 elements
Group 4 (   Backbone) has   474 elements
Group 5 (  MainChain) has   633 elements
Group 6 (   MainChain+Cb) has   779 elements
Group 7 (MainChain+H) has   789 elements
Group 8 (  SideChain) has   728 elements
Group 9 (SideChain-H) has   566 elements
Group10 (Prot-Masses) has  1517 elements
Group11 (non-Protein) has 209021 elements
Group12 (  Other) has  6200 elements
Group13 (   DPPC) has  6200 elements
Group14 ( CL) has21 elements
Group15 (  Water) has 202800 elements
Group16 (SOL) has 202800 elements
Group17 (  non-Water) has  7738 elements
Group18 (Ion) has21 elements
Group19 (   DPPC) has  6200 elements
Group20 ( CL) has21 elements
Group21 ( Water_and_ions) has 202821 elements

Select a group: 1
Selected 1: 'Protein'
*Select a group: ? (Which I want Select)*

kindly provide answers

Thanking You In Advance



-- 
*S.VENKATESH,*
Tamil Nadu,India
-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] g_sas doubt -reg

2012-09-02 Thread Justin Lemkul




On 9/2/12 2:10 PM, venkatesh s wrote:

Dear Sir / Madam,
  I want run Solvent accessible surface area in
gromacs,i aware about  g_sas is there but for selecting group little bit
confusing

Reading frame   0 time0.000   Select a group for calculation of
surface and a group for output:
Group 0 ( System) has 210538 elements
Group 1 (Protein) has  1517 elements
Group 2 (  Protein-H) has  1199 elements
Group 3 (C-alpha) has   158 elements
Group 4 (   Backbone) has   474 elements
Group 5 (  MainChain) has   633 elements
Group 6 (   MainChain+Cb) has   779 elements
Group 7 (MainChain+H) has   789 elements
Group 8 (  SideChain) has   728 elements
Group 9 (SideChain-H) has   566 elements
Group10 (Prot-Masses) has  1517 elements
Group11 (non-Protein) has 209021 elements
Group12 (  Other) has  6200 elements
Group13 (   DPPC) has  6200 elements
Group14 ( CL) has21 elements
Group15 (  Water) has 202800 elements
Group16 (SOL) has 202800 elements
Group17 (  non-Water) has  7738 elements
Group18 (Ion) has21 elements
Group19 (   DPPC) has  6200 elements
Group20 ( CL) has21 elements
Group21 ( Water_and_ions) has 202821 elements

Select a group: 1
Selected 1: 'Protein'
*Select a group: ? (Which I want Select)*

kindly provide answers



From g_sas -h:

The program will ask for a group for the surface calculation and a group for 
the output. The calculation group should always consists of all the non-solvent 
atoms in the system. The output group can be the whole or part of the 
calculation group.


-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

[gmx-users] g_sas

2012-06-06 Thread Meisam Rezaei

Hi Gromacs Users

I want to plot SAS of residues with errobar.
I want to know what is the meaning of third column in file of residue.xvg
(output of g_sas)?
 which of the following expression is true about third column?
1) first answer=sqrt(summation(s_i - s_mean)/(N-1)))
2) second answer= first answer/sqrt(N)

N is the total number of frames.
In other words, is it necessary that third column be divided by sqrt(N)?
Thanks for your response.


Meisam
-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] g_sas; could not find a Van der Waals radius

2012-03-17 Thread Justin A. Lemkul




afsaneh maleki wrote:

Hi,
I have a system that is contained of Protein-DOPC-SOL-Ions. I want to
calculate residue SAS of protein.The calculation group consists of all
the non-solvent atoms in the system (37 residue Protein+ 125 DOPC+14
ion),and then protein for output. Force files used for protein and
DOPC are ffg53a6 and Berger respectively.

When I use g_sas I obtain the following message:
WARNING: could not find a Van der Waals radius for 125 atoms.

I have two questions.
Q1- This warning is important?


Well, you're trying to calculate SASA and g_sas doesn't know how to incorporate 
P atoms into that calculation, so my guess is that yes, this warning is quite 
important.



Q2-Is the valid source to get data for Van der Waals radius of
phosphorous atom to insert in the vdwradii.dat file? I think this
warning is about phosphorous atoms of DOPC. what is  Van der Waals
radius of phosphorous atoms that will be right for this goal?



The vdwradii.dat file is the correct place for this information.  The data 
presently there lack references, and there has been a lot of discussion in the 
past on whether or not these values are reliable.


-Justin

--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.

Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] g_sas

2012-03-16 Thread afsaneh maleki

Hi,

Thanks dear Justin for useful reply,

I have a system that is contained of protein-water-ions. I want to
calculate residue SAS of protein. In the first way, I select a group
consisting protein for calculation, and then this protein for output.
At the second way, I select the whole system first for calculation,
and then protein for output. The SAS_calculations of residue protein
are different in two ways.
I have two questions.

Q1- Why results are different in two ways?
Q2-Can anyone demonstrates clearly how residue SAS of protein
calculate in two ways?
Q3- what property or quantity do I can get from The SAS_calculations
of residue protein in two ways?

Best wishes,
Afsaneh


On 3/15/12, Justin A. Lemkul jalem...@vt.edu wrote:


 afsaneh maleki wrote:
 Hello dear user,

 I have a system that is contained protein-water-ions. I used the
 following command:
 g_sas -f  free.xtc  -s  free.tpr   -o area  -or  res_area -oa
 atom_area –q -nopbc

 I select the whole protein first for calculation, and then this protein
 for output.In this way I can obtain Area per residue from res_area file
 and
 area per atom from atom_area file.

 How to get area per residue with data of area per atom from atom_area
 file? When I average on area per atoms for a selected residue, it
 doesn't correspond with area per residue for a selected residue from
 res_area.

 It shouldn't.  Averaging the areas per atom should not produce anything
 related
 to the constituent residue(s).  The sum of the atom areas should yield the
 residue area.  A quick look through the code seems to indicate that this is
 true, that is, the two quantities are not produced independently; residue
 area
 arises from atom area.

 -Justin

 How to correlate area per residue for a selected residue with area per
 atoms for a selected residue?

 Thanks in advance,
 Afsaneh

 --
 

 Justin A. Lemkul
 Ph.D. Candidate
 ICTAS Doctoral Scholar
 MILES-IGERT Trainee
 Department of Biochemistry
 Virginia Tech
 Blacksburg, VA
 jalemkul[at]vt.edu | (540) 231-9080
 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

 
 --
 gmx-users mailing listgmx-users@gromacs.org
 http://lists.gromacs.org/mailman/listinfo/gmx-users
 Please search the archive at
 http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
 Please don't post (un)subscribe requests to the list. Use the
 www interface or send it to gmx-users-requ...@gromacs.org.
 Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] g_sas

2012-03-16 Thread Justin A. Lemkul




afsaneh maleki wrote:

Hi,

Thanks dear Justin for useful reply,

I have a system that is contained of protein-water-ions. I want to
calculate residue SAS of protein. In the first way, I select a group
consisting protein for calculation, and then this protein for output.
At the second way, I select the whole system first for calculation,
and then protein for output. The SAS_calculations of residue protein
are different in two ways.
I have two questions.

Q1- Why results are different in two ways?


You're asking g_sas to do two different things.  You should note that g_sas 
tells you precisely how to do the calculation (from g_sas -h):


The calculation group should always consists of all the non-solvent atoms in 
the system. The output group can be the whole or part of the calculation group.


Choosing the whole system for the calculation group is wrong and will give an 
answer that is likely not what is needed.



Q2-Can anyone demonstrates clearly how residue SAS of protein
calculate in two ways?


Refer to the literature cited in the g_sas screen output.  Those papers will 
contain the methods.  Your second method is, however, not appropriate.  The 
first method is.



Q3- what property or quantity do I can get from The SAS_calculations
of residue protein in two ways?



Likely a meaningful one and a useless one.

-Justin

--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.

Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

[gmx-users] g_sas; could not find a Van der Waals radius

2012-03-16 Thread afsaneh maleki

Hi,
I have a system that is contained of Protein-DOPC-SOL-Ions. I want to
calculate residue SAS of protein.The calculation group consists of all
the non-solvent atoms in the system (37 residue Protein+ 125 DOPC+14
ion),and then protein for output. Force files used for protein and
DOPC are ffg53a6 and Berger respectively.

When I use g_sas I obtain the following message:
WARNING: could not find a Van der Waals radius for 125 atoms.

I have two questions.
Q1- This warning is important?
Q2-Is the valid source to get data for Van der Waals radius of
phosphorous atom to insert in the vdwradii.dat file? I think this
warning is about phosphorous atoms of DOPC. what is  Van der Waals
radius of phosphorous atoms that will be right for this goal?

Thanks very much in advance,
afsaneh
-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

[gmx-users] g_sas

2012-03-15 Thread afsaneh maleki

Hello dear user,

I have a system that is contained protein-water-ions. I used the
following command:
g_sas -f  free.xtc  -s  free.tpr   -o area  -or  res_area -oa
atom_area –q -nopbc

I select the whole protein first for calculation, and then this protein
for output.In this way I can obtain Area per residue from res_area file and
area per atom from atom_area file.

How to get area per residue with data of area per atom from atom_area
file? When I average on area per atoms for a selected residue, it
doesn't correspond with area per residue for a selected residue from
res_area.
How to correlate area per residue for a selected residue with area per
atoms for a selected residue?

Thanks in advance,
Afsaneh
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] g_sas

2012-03-15 Thread Justin A. Lemkul




afsaneh maleki wrote:

Hello dear user,

I have a system that is contained protein-water-ions. I used the
following command:
g_sas -f  free.xtc  -s  free.tpr   -o area  -or  res_area -oa
atom_area –q -nopbc

I select the whole protein first for calculation, and then this protein
for output.In this way I can obtain Area per residue from res_area file and
area per atom from atom_area file.

How to get area per residue with data of area per atom from atom_area
file? When I average on area per atoms for a selected residue, it
doesn't correspond with area per residue for a selected residue from
res_area.


It shouldn't.  Averaging the areas per atom should not produce anything related 
to the constituent residue(s).  The sum of the atom areas should yield the 
residue area.  A quick look through the code seems to indicate that this is 
true, that is, the two quantities are not produced independently; residue area 
arises from atom area.


-Justin


How to correlate area per residue for a selected residue with area per
atoms for a selected residue?

Thanks in advance,
Afsaneh


--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.

Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

[gmx-users] g_sas

2012-03-14 Thread afsaneh maleki

Dear user,

I have a system that is contained of protein-water-ions. There, I
select the whole protein first for calculation, and then this protein
for output. I used the following command:
g_sas -f  free.xtc  -s  free.tpr   -o area  -or  res_area -oa
atom_area –q -nopbc

In this way I can obtain Area per residue from res_area file and
area per atom from atom_area file.

How to get area per residue by data of area per atom from atom_area
file? When I average on area per atoms for a selected residue, it
doesn't correspond with area per residue for a selected residue from
res_area.
How to correlate area per residue for a selected residue with area per
atoms for a selected residue?

Thanks in advance,
Afsaneh
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

[gmx-users] g_sas vdwradii.dat

2011-12-30 Thread afsaneh maleki

Hi,

I finished the simulation of a peptide in DOPC bilayer in according to
tutorial by Dr. Justin.
I had not added van der Waals radius of phosphorous in the
vdwradii.dat file, when I did simulation. It seem that it use the default
value of 0.12 nm.
When I use g_sas command, I get the following warning:

WARNING: could not find a Van der Waals radius for 125 atoms

I have two questions.

Q1) Can I add radius of van der Waals of phosphorous in vdwradii.dat after
simulation?  or should i repeat simulation again?

I couldn't find the reference that report radius of van der Waals for
elements like what is in vwdradii.dat. For example see this address
http://www.webelements.com
Q2) would you please get me exact reference to find radius of van der
Waals of phosphor that match with other elements in vdwradii.dat?

Thanks in advance
-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] g_sas vdwradii.dat

2011-12-30 Thread Mark Abraham


On 31/12/2011 5:04 PM, afsaneh maleki wrote:

Hi,

I finished the simulation of a peptide in DOPC bilayer in according to
tutorial by Dr. Justin.
I had not added van der Waals radius of phosphorous in the
vdwradii.dat file, when I did simulation. It seem that it use the default
value of 0.12 nm.
When I use g_sas command, I get the following warning:

WARNING: could not find a Van der Waals radius for 125 atoms

I have two questions.

Q1) Can I add radius of van der Waals of phosphorous in vdwradii.dat 
after simulation?  or should i repeat simulation again?


The simulation does not care about that file. Only the analysis routine 
cares.




I couldn't find the reference that report radius of van der Waals for
elements like what is in vwdradii.dat. For example see this address
http://www.webelements.com
Q2) would you please get me exact reference to find radius of van der
Waals of phosphor that match with other elements in vdwradii.dat?


Don't know.

Mark


Thanks in advance




-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

[gmx-users] g_sas of ligands

2011-09-09 Thread Steven Neumann

Dear Gromacs Users,

I am calculating SAS using g_sas of ligands in my system: protein, 30
ligands in water. The hydrophobic SAS of ligands decrease and reach stable
value. Hydrophilic remains stable over the simulation time. I am wondering
whether it  (the decrease o hydrophobic) is because of binding to protein or
aggregations of my small molecules (They do aggregate) or both? I mean: how
is it caculated? Is binding to protein included in the decrease of the
hydrophobic SAS of lignads or it is impossible and  aggregation will be the
one thing?

Thank you,
-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

[gmx-users] g_sas

2011-09-08 Thread Smolin, Nikolai

Dear All,

I am wondering what kind of volume computed by g_sas?
volume inside SAS or inside contact surface (Connoly volume)?

Best regards,
Thanks

Nikolai

-- 
-
Dr. Nikolai Smolin
Postdoctoral Research Associate,
UT/ORNL Center for Molecular Biophysics, Oak Ridge National Laboratory
P.O.Box 2008 Oak Ridge TN 37831-6164, USA.
Building 6011, room 233,
Tel: (865) 241-5237, (865) 241-5192
Fax   : (865) 576-7651
E-mail : nikolai.smo...@gmail.com
http://cmb.ornl.gov/group/smolinn
http://sites.google.com/site/nikolaismolin/
-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

[gmx-users] g_sas of ligands

2011-09-08 Thread Steven Neumann

Dear Gromacs Users,

I am calculating SAS using g_sas of ligands in my system: protein, 30
ligands in water. The hydrophobic SAS of ligands decrease and reach stable
value. Hydrophilic remains stable over the simulation time. I am wondering
whether it  (the decrease o hydrophobic) is because of binding to protein or
aggregations of my small molecules (They do aggregate) or both? I mean: how
is it caculated? Is binding to protein included in the decrease of the
hydrophobic SAS of lignads or it is impossible and  aggregation will be the
one thing?

Thank you,

Steven
-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

[gmx-users] g_sas calculation

2011-07-03 Thread ahmet yıldırım

Dear users,

I want to compute SASA between protein and ligand.
*1.)*
protein and ligand are merged by make_ndx
g_sas -f run.xtc -s run.tpr -o protein_ligand.xvg -n protein_ligand.ndx
Select a group for calculation of surface and a group for output
select a group: 1 (protein+ligand)
select a group: 2 (ligand)
is this correct?

*2.)*
or
g_sas -f run.xtc -s run.tpr -o protein_protein.xvg
Select a group for calculation of surface and a group for output
select a group: 1 (protein)
select a group: 2 (protein)
I have protein SASA.

g_sas -f run.xtc -s run.tpr -o ligand_ligand.xvg
Select a group for calculation of surface and a group for output
select a group: 1 (ligand)
select a group: 2 (ligand)
I have ligand SASA.

protein and ligand are merged by make_ndx
g_sas -f run.xtc -s run.tpr -o protein_ligand.xvg -n protein_ligand.ndx
Select a group for calculation of surface and a group for output
select a group: 1 (protein_ligand)
select a group: 2 (protein_ligand)
I have protein_ligand SASA.

(SASA between protein and ligand)=(protein)+(ligand)-(protein_ligand)

I am confused. which of choices is correct?

Thanks in advance

-- 
Ahmet YILDIRIM
-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] g_sas calculation

2011-07-03 Thread Justin A. Lemkul




ahmet yıldırım wrote:

Dear users,

I want to compute SASA between protein and ligand.
*1.)*
protein and ligand are merged by make_ndx
g_sas -f run.xtc -s run.tpr -o protein_ligand.xvg -n protein_ligand.ndx
Select a group for calculation of surface and a group for output
select a group: 1 (protein+ligand)
select a group: 2 (ligand)
is this correct?

*2.)*
or
g_sas -f run.xtc -s run.tpr -o protein_protein.xvg
Select a group for calculation of surface and a group for output
select a group: 1 (protein)
select a group: 2 (protein)
I have protein SASA.

g_sas -f run.xtc -s run.tpr -o ligand_ligand.xvg
Select a group for calculation of surface and a group for output
select a group: 1 (ligand)
select a group: 2 (ligand)
I have ligand SASA.

protein and ligand are merged by make_ndx
g_sas -f run.xtc -s run.tpr -o protein_ligand.xvg -n protein_ligand.ndx
Select a group for calculation of surface and a group for output
select a group: 1 (protein_ligand)
select a group: 2 (protein_ligand)
I have protein_ligand SASA.

(SASA between protein and ligand)=(protein)+(ligand)-(protein_ligand)

I am confused. which of choices is correct?



Neither.  Your equation is right, but your method of calculating each of the 
quantities is not.  The group for the surface calculation should always be all 
non-solvent atoms (per the instructions in g_sas -h).  The output group can then 
be whatever you like, a subset of that surface.  So you will need three 
calculations (sort of like option #2), but in each case the calculation group 
should always be the protein-ligand merged group.


-Justin

--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.

Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] g_sas calculation

2011-07-03 Thread ahmet yıldırım

Dear Justin,

Firstly thanks for your valuable information. Now, is there any error?
Please see the following commands:

protein and ligand are merged by make_ndx

g_sas -f run.xtc -s run.tpr -o area_protein.xvg -n protein_ligand.ndx
Select a group for calculation of surface and a group for output
*select a group: 1 (protein_ligand)*
*select a group: 2 (protein)*
*I have protein SASA.*

g_sas -f run.xtc -s run.tpr -o area_ligand.xvg -n protein_ligand.ndx
Select a group for calculation of surface and a group for output
*select a group: 1 (protein_ligand)*
*select a group: 2 (ligand)
I have ligand SASA.*

g_sas -f run.xtc -s run.tpr -o area_protein_ligand.xvg -n protein_ligand.ndx
Select a group for calculation of surface and a group for output
*select a group: 1 (protein_ligand)*
*select a group: 2 (protein_ligand)
I have protein_ligand SASA.*

*(SASA between protein and ligand)=(protein)+(ligand)-(protein_ligand)*

Thanks

2011/7/3 Justin A. Lemkul jalem...@vt.edu



 ahmet yıldırım wrote:

 Dear users,

 I want to compute SASA between protein and ligand.
 *1.)*
 protein and ligand are merged by make_ndx
 g_sas -f run.xtc -s run.tpr -o protein_ligand.xvg -n protein_ligand.ndx
 Select a group for calculation of surface and a group for output
 select a group: 1 (protein+ligand)
 select a group: 2 (ligand)
 is this correct?

 *2.)*
 or
 g_sas -f run.xtc -s run.tpr -o protein_protein.xvg
 Select a group for calculation of surface and a group for output
 select a group: 1 (protein)
 select a group: 2 (protein)
 I have protein SASA.

 g_sas -f run.xtc -s run.tpr -o ligand_ligand.xvg
 Select a group for calculation of surface and a group for output
 select a group: 1 (ligand)
 select a group: 2 (ligand)
 I have ligand SASA.

 protein and ligand are merged by make_ndx
 g_sas -f run.xtc -s run.tpr -o protein_ligand.xvg -n protein_ligand.ndx
 Select a group for calculation of surface and a group for output
 select a group: 1 (protein_ligand)
 select a group: 2 (protein_ligand)
 I have protein_ligand SASA.

 (SASA between protein and ligand)=(protein)+(ligand)-(**protein_ligand)

 I am confused. which of choices is correct?


 Neither.  Your equation is right, but your method of calculating each of
 the quantities is not.  The group for the surface calculation should always
 be all non-solvent atoms (per the instructions in g_sas -h).  The output
 group can then be whatever you like, a subset of that surface.  So you will
 need three calculations (sort of like option #2), but in each case the
 calculation group should always be the protein-ligand merged group.

 -Justin

 --
 ==**==

 Justin A. Lemkul
 Ph.D. Candidate
 ICTAS Doctoral Scholar
 MILES-IGERT Trainee
 Department of Biochemistry
 Virginia Tech
 Blacksburg, VA
 jalemkul[at]vt.edu | (540) 231-9080
 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

 ==**==
 --
 gmx-users mailing listgmx-users@gromacs.org
 http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users
 Please search the archive at http://www.gromacs.org/**
 Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore
  posting!
 Please don't post (un)subscribe requests to the list. Use the www interface
 or send it to gmx-users-requ...@gromacs.org.
 Can't post? Read 
 http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists




-- 
Ahmet YILDIRIM
-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] g_sas calculation

2011-07-03 Thread Justin A. Lemkul




ahmet yıldırım wrote:

Dear Justin,

Firstly thanks for your valuable information. Now, is there any error?
Please see the following commands:

protein and ligand are merged by make_ndx

g_sas -f run.xtc -s run.tpr -o area_protein.xvg -n protein_ligand.ndx
Select a group for calculation of surface and a group for output
*select a group: 1 (protein_ligand)*
*select a group: 2 (protein)*
*I have protein SASA.*

g_sas -f run.xtc -s run.tpr -o area_ligand.xvg -n protein_ligand.ndx
Select a group for calculation of surface and a group for output
*select a group: 1 (protein_ligand)*
*select a group: 2 (ligand)
I have ligand SASA.*

g_sas -f run.xtc -s run.tpr -o area_protein_ligand.xvg -n protein_ligand.ndx
Select a group for calculation of surface and a group for output
*select a group: 1 (protein_ligand)*
*select a group: 2 (protein_ligand)
I have protein_ligand SASA.*

*(SASA between protein and ligand)=(protein)+(ligand)-(protein_ligand)*



I'm sorry, I read the first post wrong.  Your equation will yield an answer of 
zero if you do this.  I was thinking of your problem backwards.  You do indeed 
want to calculate all of these quantities individually, as you proposed in 
method #2 previously.  That way, you can get the interior cavity surface area, 
not the exterior components as I was thinking.


-Justin


Thanks

2011/7/3 Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu



ahmet yıldırım wrote:

Dear users,

I want to compute SASA between protein and ligand.
*1.)*
protein and ligand are merged by make_ndx
g_sas -f run.xtc -s run.tpr -o protein_ligand.xvg -n
protein_ligand.ndx
Select a group for calculation of surface and a group for output
select a group: 1 (protein+ligand)
select a group: 2 (ligand)
is this correct?

*2.)*
or
g_sas -f run.xtc -s run.tpr -o protein_protein.xvg
Select a group for calculation of surface and a group for output
select a group: 1 (protein)
select a group: 2 (protein)
I have protein SASA.

g_sas -f run.xtc -s run.tpr -o ligand_ligand.xvg
Select a group for calculation of surface and a group for output
select a group: 1 (ligand)
select a group: 2 (ligand)
I have ligand SASA.

protein and ligand are merged by make_ndx
g_sas -f run.xtc -s run.tpr -o protein_ligand.xvg -n
protein_ligand.ndx
Select a group for calculation of surface and a group for output
select a group: 1 (protein_ligand)
select a group: 2 (protein_ligand)
I have protein_ligand SASA.

(SASA between protein and
ligand)=(protein)+(ligand)-(__protein_ligand)

I am confused. which of choices is correct?


Neither.  Your equation is right, but your method of calculating
each of the quantities is not.  The group for the surface
calculation should always be all non-solvent atoms (per the
instructions in g_sas -h).  The output group can then be whatever
you like, a subset of that surface.  So you will need three
calculations (sort of like option #2), but in each case the
calculation group should always be the protein-ligand merged group.

-Justin

-- 
==__==


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu http://vt.edu | (540) 231-9080
http://www.bevanlab.biochem.__vt.edu/Pages/Personal/justin
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

==__==
-- 
gmx-users mailing listgmx-users@gromacs.org

mailto:gmx-users@gromacs.org
http://lists.gromacs.org/__mailman/listinfo/gmx-users
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/__Support/Mailing_Lists/Search
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the www
interface or send it to gmx-users-requ...@gromacs.org
mailto:gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/__Support/Mailing_Lists
http://www.gromacs.org/Support/Mailing_Lists




--
Ahmet YILDIRIM


--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www

Re: [gmx-users] g_sas calculation

2011-07-03 Thread Justin A. Lemkul




Justin A. Lemkul wrote:



ahmet yıldırım wrote:

Dear Justin,

Firstly thanks for your valuable information. Now, is there any error?
Please see the following commands:

protein and ligand are merged by make_ndx

g_sas -f run.xtc -s run.tpr -o area_protein.xvg -n protein_ligand.ndx
Select a group for calculation of surface and a group for output
*select a group: 1 (protein_ligand)*
*select a group: 2 (protein)*
*I have protein SASA.*

g_sas -f run.xtc -s run.tpr -o area_ligand.xvg -n protein_ligand.ndx
Select a group for calculation of surface and a group for output
*select a group: 1 (protein_ligand)*
*select a group: 2 (ligand)
I have ligand SASA.*

g_sas -f run.xtc -s run.tpr -o area_protein_ligand.xvg -n 
protein_ligand.ndx

Select a group for calculation of surface and a group for output
*select a group: 1 (protein_ligand)*
*select a group: 2 (protein_ligand)
I have protein_ligand SASA.*

*(SASA between protein and ligand)=(protein)+(ligand)-(protein_ligand)*



I'm sorry, I read the first post wrong.  Your equation will yield an 
answer of zero if you do this.  I was thinking of your problem 
backwards.  You do indeed want to calculate all of these quantities 
individually, as you proposed in method #2 previously.  That way, you 
can get the interior cavity surface area, not the exterior components as 
I was thinking.




In addition, this gives the buried surface area, which is actually twice the 
interfacial surface area.  Both can be useful to understand (the former for 
analyzing the free energy change of burying these surfaces and the latter for 
the actual level of contact between the protein and ligand).


-Justin

--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.

Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

[gmx-users] g_sas index files/hydrogen bonds

2011-06-14 Thread Marzinek, Jan

Dear Gromacs Users,

I am calculating the hydrophobic interface area using g_sas between ligands 
(their hydrophobic solvent accessible surface area (SASA) 95%) and hydrophobic 
residues of coiled coil fragment of protein (two helical strands) as follows:

Protein SASA + ligand SASA - ProteinLigand SASA = Interface Area between 
ligands protein

I obtained the hydrophobic interface area increasing during the simulation time 
- so everything seems to be ok, because from my simulation 10 ligands occupy 
hydrophobic residues (the helical terminal strands open allowing ligands to 
come inside the protein).
However, 10 ligands aggregates during the simulation covering their hydrophobic 
surface which obviously has the influence on the final interface between 
protein and ligands.
Do you know how to calculate the interface area between all 10 ligands during 
the simulation time in order to subtract from final result? How should I define 
index files?

The second question: I also calculated the hydrogen bonds between ligands and 
the protein. What is interesting: app. 70% of hydrogen bonds between 
hydrophobic ligands are formed with HYDROPHILIC residues of protein. Any clue 
what is happening as final conformation involve ligands between hydrophobic 
surfaces of the protein?

All the best,

Jan
-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] g_sas query

2011-05-07 Thread Tsjerk Wassenaar

Hey Anirban,

I would consider the ions part of the solvent. But the procedure is right.

Cheers,

Tsjerk

On May 7, 2011 7:35 AM, Anirban Ghosh reach.anirban.gh...@gmail.com
wrote:

Hi ALL,

I want to calculate the SASA of a protein embedded in a bilayer along with
water and ions. So while using g_sas I understand that I need to supply all
non-solvent atoms as calculation group and Protein as the output group. So I
need to make a group with Protein+Lipid+Ions as the calculation group.
Right?
Thanks a lot in advance.

Regards,

Anirban

--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] g_sas query

2011-05-07 Thread Anirban Ghosh

Hello Tsjerk,

Thanks for the reply.
But if I consider the ions also in the calculation group, then it is not
wrong. Right?

Thanks,

Anirban

On Sat, May 7, 2011 at 11:59 AM, Tsjerk Wassenaar tsje...@gmail.com wrote:

 Hey Anirban,

 I would consider the ions part of the solvent. But the procedure is right.

 Cheers,

 Tsjerk

 On May 7, 2011 7:35 AM, Anirban Ghosh reach.anirban.gh...@gmail.com
 wrote:

 Hi ALL,

 I want to calculate the SASA of a protein embedded in a bilayer along with
 water and ions. So while using g_sas I understand that I need to supply all
 non-solvent atoms as calculation group and Protein as the output group. So I
 need to make a group with Protein+Lipid+Ions as the calculation group.
 Right?
 Thanks a lot in advance.

 Regards,

 Anirban

 --
 gmx-users mailing listgmx-users@gromacs.org
 http://lists.gromacs.org/mailman/listinfo/gmx-users
 Please search the archive at
 http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
 Please don't post (un)subscribe requests to the list. Use the
 www interface or send it to gmx-users-requ...@gromacs.org.
 Can't post? Read http://www.gromacs.org/Support/Mailing_Lists


 --
 gmx-users mailing listgmx-users@gromacs.org
 http://lists.gromacs.org/mailman/listinfo/gmx-users
 Please search the archive at
 http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
 Please don't post (un)subscribe requests to the list. Use the
 www interface or send it to gmx-users-requ...@gromacs.org.
 Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] g_sas query

2011-05-07 Thread Mark Abraham


On 7/05/2011 4:36 PM, Anirban Ghosh wrote:

Hello Tsjerk,

Thanks for the reply.
But if I consider the ions also in the calculation group, then it is 
not wrong. Right?


Only you know where your ions are, and whether their contribution to 
surface area means anything. Make the hybrid groups accordingly.


Mark


Thanks,

Anirban

On Sat, May 7, 2011 at 11:59 AM, Tsjerk Wassenaar tsje...@gmail.com 
mailto:tsje...@gmail.com wrote:


Hey Anirban,

I would consider the ions part of the solvent. But the procedure
is right.

Cheers,

Tsjerk


On May 7, 2011 7:35 AM, Anirban Ghosh
reach.anirban.gh...@gmail.com
mailto:reach.anirban.gh...@gmail.com wrote:

Hi ALL,

I want to calculate the SASA of a protein embedded in a bilayer
along with water and ions. So while using g_sas I understand that
I need to supply all non-solvent atoms as calculation group and
Protein as the output group. So I need to make a group with
Protein+Lipid+Ions as the calculation group. Right?
Thanks a lot in advance.

Regards,

Anirban

--
gmx-users mailing list gmx-users@gromacs.org
mailto:gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org
mailto:gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists


--
gmx-users mailing list gmx-users@gromacs.org
mailto:gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org
mailto:gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists





-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] g_sas query

2011-05-07 Thread Anirban Ghosh

Hello Tsjerk  Mark,

Thanks for the reply.
Actually more important than the ions is the lipid bilayer of my system.
Actually my protein is a GPCR embedded in a lipid bilayer. So when I want to
calculate the SASA of my protein, so should I use a group
(Protein+Lipid+Ions) as the calculation group and Protein as the output
group?

Thanks again,

Anirban

On Sat, May 7, 2011 at 1:05 PM, Mark Abraham mark.abra...@anu.edu.auwrote:

  On 7/05/2011 4:36 PM, Anirban Ghosh wrote:

 Hello Tsjerk,

  Thanks for the reply.
 But if I consider the ions also in the calculation group, then it is not
 wrong. Right?


 Only you know where your ions are, and whether their contribution to
 surface area means anything. Make the hybrid groups accordingly.

 Mark


  Thanks,

  Anirban

 On Sat, May 7, 2011 at 11:59 AM, Tsjerk Wassenaar tsje...@gmail.comwrote:

 Hey Anirban,

 I would consider the ions part of the solvent. But the procedure is right.

 Cheers,

 Tsjerk

  On May 7, 2011 7:35 AM, Anirban Ghosh reach.anirban.gh...@gmail.com
 wrote:

 Hi ALL,

  I want to calculate the SASA of a protein embedded in a bilayer along
 with water and ions. So while using g_sas I understand that I need to supply
 all non-solvent atoms as calculation group and Protein as the output group.
 So I need to make a group with Protein+Lipid+Ions as the calculation group.
 Right?
 Thanks a lot in advance.

  Regards,

  Anirban

  --
 gmx-users mailing listgmx-users@gromacs.org
 http://lists.gromacs.org/mailman/listinfo/gmx-users
 Please search the archive at
 http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
 Please don't post (un)subscribe requests to the list. Use the
 www interface or send it to gmx-users-requ...@gromacs.org.
 Can't post? Read http://www.gromacs.org/Support/Mailing_Lists


 --
 gmx-users mailing listgmx-users@gromacs.org
 http://lists.gromacs.org/mailman/listinfo/gmx-users
 Please search the archive at
 http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
 Please don't post (un)subscribe requests to the list. Use the
 www interface or send it to gmx-users-requ...@gromacs.org.
 Can't post? Read http://www.gromacs.org/Support/Mailing_Lists





 --
 gmx-users mailing listgmx-users@gromacs.org
 http://lists.gromacs.org/mailman/listinfo/gmx-users
 Please search the archive at
 http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
 Please don't post (un)subscribe requests to the list. Use the
 www interface or send it to gmx-users-requ...@gromacs.org.
 Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] g_sas query

2011-05-07 Thread Mark Abraham


On 7/05/2011 7:04 PM, Anirban Ghosh wrote:

Hello Tsjerk  Mark,

Thanks for the reply.
Actually more important than the ions is the lipid bilayer of my 
system. Actually my protein is a GPCR embedded in a lipid bilayer. So 
when I want to calculate the SASA of my protein, so should I use a 
group (Protein+Lipid+Ions) as the calculation group and Protein as the 
output group?


We've answered the first part of this already.

You should read g_sas -h for clues about the groups. Only you know 
whether Protein-only output is sensible for your purpose.


Mark


Thanks again,

Anirban

On Sat, May 7, 2011 at 1:05 PM, Mark Abraham mark.abra...@anu.edu.au 
mailto:mark.abra...@anu.edu.au wrote:


On 7/05/2011 4:36 PM, Anirban Ghosh wrote:

Hello Tsjerk,

Thanks for the reply.
But if I consider the ions also in the calculation group, then it
is not wrong. Right?


Only you know where your ions are, and whether their contribution
to surface area means anything. Make the hybrid groups accordingly.

Mark



Thanks,

Anirban

On Sat, May 7, 2011 at 11:59 AM, Tsjerk Wassenaar
tsje...@gmail.com mailto:tsje...@gmail.com wrote:

Hey Anirban,

I would consider the ions part of the solvent. But the
procedure is right.

Cheers,

Tsjerk


On May 7, 2011 7:35 AM, Anirban Ghosh
reach.anirban.gh...@gmail.com
mailto:reach.anirban.gh...@gmail.com wrote:

Hi ALL,

I want to calculate the SASA of a protein embedded in a
bilayer along with water and ions. So while using g_sas I
understand that I need to supply all non-solvent atoms as
calculation group and Protein as the output group. So I need
to make a group with Protein+Lipid+Ions as the calculation
group. Right?
Thanks a lot in advance.

Regards,

Anirban

--
gmx-users mailing list gmx-users@gromacs.org
mailto:gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before
posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org
mailto:gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists


--
gmx-users mailing list gmx-users@gromacs.org
mailto:gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before
posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org
mailto:gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists






--
gmx-users mailing list gmx-users@gromacs.org
mailto:gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org
mailto:gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists




-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

[gmx-users] g_sas query

2011-05-06 Thread Anirban Ghosh

Hi ALL,

I want to calculate the SASA of a protein embedded in a bilayer along with
water and ions. So while using g_sas I understand that I need to supply all
non-solvent atoms as calculation group and Protein as the output group. So I
need to make a group with Protein+Lipid+Ions as the calculation group.
Right?
Thanks a lot in advance.

Regards,

Anirban
-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

[gmx-users] g_sas and g_rdf

2010-11-15 Thread Carla Jamous

Hi everyone,

I'm trying to look at the radial distribution function of water around the
surface of my protein. For that, I calculated the surface area per residue
(g_sas -or).
Since I didn't find in the litterature any criteria to choose a minimum area
value to count a residue as a a surface residue, I chose to analyze the
residues that have an area value  1.3 nm2

I counted 23 residues that have area values  1.3 nm2

I made an index file with one index group for each residue and on index
group for SOL_OW
Then I ran g_rdf on my trajectory
g_rdf -s .tpr -f .xtc -n .ndx -o rdf.xvg -bin  0.02 -com
I chose: reference group=the residue I want to analyze
 group = SOL_OW

even though I'm analyzing the residues that have large surface area values,
my RDF plot doesn't look like what I was execting: it means an RDF plot with
a peak at g(r)=2 or 3 then a decrease in g(r) and finally a g(r)=1
My peak is at g(r)=0.7 and then it increases to g(r)=1

Does anyone have an idea why I have this kind of plot? Because I didn't find
any answers in the mailing list.

Thank you,
Carla
-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] g_sas resarea.xvg

2010-11-06 Thread Mark Abraham


On 4/11/2010 11:04 PM, Justin A. Lemkul wrote:



Carla Jamous wrote:

Hi everyone,

I used g_sas: g_sas -s .tpr -f .xtc -n .ndx -o .xvg -or resarea.xvg

What I don't understand is why there are 3 columns in the file 
resarea.xvg although this is what's written in my file:

# g_sas is part of G R O M A C S:
#
# GROtesk MACabre and Sinister
#
@title Area per residue
@xaxis  label Residue
@yaxis  label Area (nm\S2\N)
@TYPE xy

So I would expect this file to contain only two columns. I'm using 
gromacs version 4.0.3.




Residue, average area, standard deviation.


Fixed in git.

Mark


-Justin


Thanks for your help,
Carla





--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.

Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

[gmx-users] g_sas resarea.xvg

2010-11-04 Thread Carla Jamous

Hi everyone,

I used g_sas: g_sas -s .tpr -f .xtc -n .ndx -o .xvg -or resarea.xvg

What I don't understand is why there are 3 columns in the file resarea.xvg
although this is what's written in my file:
# g_sas is part of G R O M A C S:
#
# GROtesk MACabre and Sinister
#
@title Area per residue
@xaxis  label Residue
@yaxis  label Area (nm\S2\N)
@TYPE xy

So I would expect this file to contain only two columns. I'm using gromacs
version 4.0.3.

Thanks for your help,
Carla
-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] g_sas resarea.xvg

2010-11-04 Thread Justin A. Lemkul




Carla Jamous wrote:

Hi everyone,

I used g_sas: g_sas -s .tpr -f .xtc -n .ndx -o .xvg -or resarea.xvg

What I don't understand is why there are 3 columns in the file 
resarea.xvg although this is what's written in my file:

# g_sas is part of G R O M A C S:
#
# GROtesk MACabre and Sinister
#
@title Area per residue
@xaxis  label Residue
@yaxis  label Area (nm\S2\N)
@TYPE xy

So I would expect this file to contain only two columns. I'm using 
gromacs version 4.0.3.




Residue, average area, standard deviation.

-Justin


Thanks for your help,
Carla



--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.

Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

[gmx-users] g_sas = protein interface = HALF of ( A+B-AB) ?

2010-08-26 Thread Chih-Ying Lin

Hi
Execute g_sas  to get  protein interface

From David =
If you have protein A and B in complex you do three g_sas:
AB AB
A A
B B
the interface is now A + B - AB


WHy not HALF of (A+B-AB)  ?

Thank you
Lin
-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php

[gmx-users] g_sas = protein interface = HALF of ( A+B-AB) ?

2010-08-26 Thread Chih-Ying Lin

Hi
Execute g_sas  to get  protein interface

From David =
If you have protein A and B in complex you do three g_sas:
AB AB
A A
B B
the interface is now A + B - AB


WHy not HALF of (A+B-AB)  ?

Thank you
Lin
-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php

[gmx-users] g_sas = calculate the SASA for each residues ?

2010-08-26 Thread Chih-Ying Lin

Hi
How can I calculate the SASA for each residue ?
From Manual = The program will ask for a group for the surface calculation
and a group for the output.



When I issue the command = g_sas -f  abc.gro   -s   abc.tpr  -n
Residue1.ndx -o SASA.xvg
= Gromacs will pick Residue1.ndx as both a group for the surface
calculation and a group for the output.



When I issue the command = g_sas -f  abc.gro   -s   abc.tpr  -n
Residue1.ndx -n protein.ndx -o SASA.xvg
= Gromacs will show = Fatal error:Double command line argument -n



I want protein.ndx as a group for the surface calculation and Residue1.ndx
as a group for the output.
How to do fix the problem ?

Thank you
Lin










Group 0 (  System) has 20659 elements
Group 1 ( Protein) has  1321 elements
Group 2 (   Protein-H) has  1001 elements
Group 3 ( C-alpha) has   129 elements
Group 4 (Backbone) has   387 elements
Group 5 (   MainChain) has   517 elements
Group 6 (MainChain+Cb) has   634 elements
Group 7 ( MainChain+H) has   646 elements
Group 8 (   SideChain) has   675 elements
Group 9 ( SideChain-H) has   484 elements
Group10 ( Prot-Masses) has  1321 elements
Group11 ( Non-Protein) has 19338 elements
Group12 ( azo) has   330 elements
Group13 ( SOL) has 19008 elements
Group14 (   Other) has 19338 elements
-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php

Re: [gmx-users] g_sas = calculate the SASA for each residues ?

2010-08-26 Thread Justin A. Lemkul




Chih-Ying Lin wrote:



Hi
How can I calculate the SASA for each residue ?
 From Manual = The program will ask for a group for the surface 
calculation and a group for the output.




When I issue the command = g_sas -f  abc.gro   -s   abc.tpr  -n 
Residue1.ndx -o SASA.xvg 
= Gromacs will pick Residue1.ndx as both a group for the surface 
calculation and a group for the output.




When I issue the command = g_sas -f  abc.gro   -s   abc.tpr  -n 
Residue1.ndx -n protein.ndx -o SASA.xvg 
= Gromacs will show = Fatal error:Double command line argument -n




I want protein.ndx as a group for the surface calculation and 
Residue1.ndx as a group for the output.

How to do fix the problem ?



You need both groups in the same index file.  As noted by the fatal error, you 
cannot supply two index files separately.


-Justin


Thank you
Lin










Group 0 (  System) has 20659 elements
Group 1 ( Protein) has  1321 elements
Group 2 (   Protein-H) has  1001 elements
Group 3 ( C-alpha) has   129 elements
Group 4 (Backbone) has   387 elements
Group 5 (   MainChain) has   517 elements
Group 6 (MainChain+Cb) has   634 elements
Group 7 ( MainChain+H) has   646 elements
Group 8 (   SideChain) has   675 elements
Group 9 ( SideChain-H) has   484 elements
Group10 ( Prot-Masses) has  1321 elements
Group11 ( Non-Protein) has 19338 elements
Group12 ( azo) has   330 elements
Group13 ( SOL) has 19008 elements
Group14 (   Other) has 19338 elements





--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.

Can't post? Read http://www.gromacs.org/mailing_lists/users.php

Re: [gmx-users] g_sas = protein interface = HALF of ( A+B-AB) ?

2010-08-26 Thread Tsjerk Wassenaar

Hi,

 the interface is now A + B - AB
 WHy not HALF of (A+B-AB)  ?

 You are right.

A + B - AB gives the Buried Surface Area, which is the amount of
surface that gets excluded from the solvent by complexation (and
consequently is twice the size of the interface).

:)

Tsjerk

-- 
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
Groningen Institute for Biomolecular Research and Biotechnology /
University of Groningen
The Netherlands
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php

Re: [gmx-users] g_sas for martini coarse-grained particles

2010-07-18 Thread XAvier Periole



the vdW radius of Martini particues is 0.263 nm, or 0.526 nm for the  
diameter.

This is clearly indicated in all the martini papers :))

On Jul 18, 2010, at 1:59 AM, Sanku M wrote:


Hi,
   I am trying to estimate the solvent accessible surface area of   
hydrophobic tails of  a martini DPPC  lipid bilayer . I was going to  
use g_sas for that. But, I observe that this tool gets the vanderwal  
radii from vdwradii.dat file. But, since the particles in the  
martini lipids are united-atom types, I was wondering what will be a  
reasonable radius to use for hydrophobic tail particles of a martini  
lipid ?


Thanks
Sanku

--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before  
posting!

Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php


-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php

Re: [gmx-users] g_sas for martini coarse-grained particles

2010-07-18 Thread XAvier Periole



also an example of the use of SASA is in JACS-2007, 129, 10126-10132

On Jul 18, 2010, at 1:59 AM, Sanku M wrote:


Hi,
   I am trying to estimate the solvent accessible surface area of   
hydrophobic tails of  a martini DPPC  lipid bilayer . I was going to  
use g_sas for that. But, I observe that this tool gets the vanderwal  
radii from vdwradii.dat file. But, since the particles in the  
martini lipids are united-atom types, I was wondering what will be a  
reasonable radius to use for hydrophobic tail particles of a martini  
lipid ?


Thanks
Sanku

--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before  
posting!

Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php


-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php

[gmx-users] g_sas for martini coarse-grained particles

2010-07-17 Thread Sanku M

Hi,
   I am trying to estimate the solvent accessible surface area of  hydrophobic 
tails of  a martini DPPC  lipid bilayer . I was going to use g_sas for that. 
But, I observe that this tool gets the vanderwal radii from vdwradii.dat file. 
But, since the particles in the martini lipids are united-atom types, I was 
wondering what will be a reasonable radius to use for hydrophobic tail 
particles 
of a martini lipid ?

Thanks
Sanku 


  -- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php

[gmx-users] g_sas

2010-05-28 Thread shahid nayeem

Dear All
Using g_sas on trajectory file with command
g_sas -f .xtc -s .tpr -oa atomarea.xvg
gives following output
   @title Area per atom  @xaxis  label Atom #  @yaxis  label
Area (nm\S2\N) @TYPE xy   1 0.139885 0.0351154  2 0.0510893 0.0236223  3
0.0510077 0.0234374  4 0.0512037 0.0234554  5 0.0284763 0.0401088  6
0.236609 0.108979
Tghe first column is atom no. and what are the values in two columns. I want
average solvent accessible surface area of each atom of my protein in whole
trajectory.
Shahid Nayeem
-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php

Re: [gmx-users] g_sas

2010-05-28 Thread Justin A. Lemkul




shahid nayeem wrote:

Dear All
Using g_sas on trajectory file with command
 g_sas -f .xtc -s .tpr -oa atomarea.xvg 


gives following output
@title Area per atom
@xaxis  label Atom #
@yaxis  label Area (nm\S2\N)
@TYPE xy
1 0.139885 0.0351154
2 0.0510893 0.0236223   
3 0.0510077 0.0234374   
4 0.0512037 0.0234554   
5 0.0284763 0.0401088   
6 0.236609 0.108979 

Tghe first column is atom no. and what are the values in two columns. I 


Average area per atom, then some sort of fluctuation term.

-Justin

want average solvent accessible surface area of each atom of my protein 
in whole trajectory.

Shahid Nayeem



--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.

Can't post? Read http://www.gromacs.org/mailing_lists/users.php

[gmx-users] g_sas command with the -q option

2010-04-15 Thread Ozge Engin

Hi all,

I have a system which is composed of hexane-peptide-water-peptide-hexane
layers. There, I selected the hexane+peptide system as the calculation
group, and the hexane group as the output group to calculate the hexane area
that is in contact with water. To do this I used the g_sas command with the
-q option. I looked at the connelly.pdb file via vmd. I think the
calculation and the output groups are shown in that file. I saw that the the
upper, right and left sides of the simulation box have been included which
means to me the periodic boundaries are not taken into account during the
calculation. In addition, when I use the g_sas command I get a warning as
the following:

WARNING: Analysis based on vacuum simulations (with the possibility of
evaporation)will certainly crash the analysis. Turning off pbc.

So, the periodic boundary is taken into account or not during the sas
calculation?

Regards
-- 
Ozge Engin
★☆
-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php

Re: [gmx-users] g_sas -pbc ???

2010-04-10 Thread Mark Abraham


On 10/04/2010 2:35 PM, Chih-Ying Lin wrote:



Hi
g_sas

By default, periodic boundary conditions are taken into account.
How does g_sas deal with periodic boundary conditions effects? ? ?


By recognizing that surfaces can cross periodic boundaries.


Take trjconv an example, I have tried trjconv -pbc ( nojump , whole,
atom... )
or, trjconv -center . I could not get what i wanted.


So how is this description supposed to get you any help? We've no idea 
what you're trying to do, what you've tried or why you think it didn't 
work. :-) Searching the mailing list for trjconv advice would have shown 
you lots of posts, along with the advice that some complex results 
require two-stage applications of trjconv to succeed.


Mark
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.

Can't post? Read http://www.gromacs.org/mailing_lists/users.php

[gmx-users] g_sas = micelle ?

2010-04-09 Thread Chih-Ying Lin

HI
how to calculate SASA of micelle using g_sas?
i put -n -micelle-index.ndx , where micelle-index.ndx includes all of the
atom numbers of micelle.


if micelle is not compact enough but there are no water molecules inside the
micelle, will g_sas calculate the vacancy part inside the micelle?

Or, if there exists water molecules inside the micelle, will g_sas calculate
the water/micelle interface part inside the micelle?


Thank you
Lin
-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php

[gmx-users] g_sas = protein and ligand aggregate interface area ?

2010-04-09 Thread Chih-Ying Lin

HI
As David said,
= How to compute protein-protein interface area?
If you have protein A and B in complex you do three g_sas:

AB AB
A A
B B

the interface is now A + B - AB



I want to calculate protein and ligand aggregate (small micelle of ligand)
interface area.
Is it the same step as calculation of protein A and B interface, which David
mentioned above?
But replacing protein B to Ligand aggregate (small micelle of ligand) ?

g_sas -n ligand-micelle-index.ndx  ?

where ligand-micelle-index.ndx includes all the atom numbers of ligand
micelle, which attached on the protein .

Is my idea correct?

Thank you
Lin
-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php

Re: [gmx-users] g_sas = protein and ligand aggregate interface area ?

2010-04-09 Thread Tsjerk Wassenaar

Hey Lin,

 Is it the same step as calculation of protein A and B interface, which David
 mentioned above?
 But replacing protein B to Ligand aggregate (small micelle of ligand) ?
 g_sas -n ligand-micelle-index.ndx  ?

Of course.

 Is my idea correct?

Is it necessary to always question your ability to think in public?
You could try and draw your problem, and you could try to see if
things turn out the way you expect them under the assumption that your
thoughts were correct.

Cheers,

Tsjerk

-- 
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
Groningen Institute for Biomolecular Research and Biotechnology
University of Groningen
The Netherlands
-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php

[gmx-users] g_sas -pbc ???

2010-04-09 Thread Chih-Ying Lin

Hi
g_sas

By default, periodic boundary conditions are taken into account.
How does g_sas deal with periodic boundary conditions effects? ? ?



Take trjconv an example, I have tried trjconv -pbc ( nojump , whole, atom...
)
or, trjconv -center . I could not get what i wanted.

Thank you
Lin
-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php

Re: [gmx-users] g_sas

2010-04-04 Thread David van der Spoel


On 2010-04-04 07.13, Chih-Ying Lin wrote:


HI
THe command =
g_sas_mpi -f 6LYZ-MD566500.xtc -s 6LYZ-MD566500.tpr -o
solvent-accessible-surface.xvg -oa atomic-sas.xvg -or residue-sas.xvg



In the solvent-accessible-surface.xvg =
@ s0 legend Hydrophobic
@ s1 legend Hydrophilic
@ s2 legend Total
@ s3 legend D Gsolv

What does Hydrophobic mean here?
What does Hydrophilic mean here?
Does Total = Hydrophobic+Hydrophilic ?
What does D Gsolv mean here?
How can Gromacs define Hydrophobic atoms and Hydrophilic atoms ?

DG solv is computed according to Eisenberg et al. See scree output for 
reference.


Hydrophobicity is determined from the charge of an atom, not a very good 
method maybe, there you can supply an index file to determine which 
residues are hydrophobic yourself.



What does the Area unit mean ? = Area (nm\S2\N)


How about square nanometer for an area?




Thank you
Lin




--
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell  Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.

Can't post? Read http://www.gromacs.org/mailing_lists/users.php

[gmx-users] g_sas

2010-04-04 Thread Chih-Ying Lin

Hi

g_sas computes hydrophobic, hydrophilic and total solvent accessible surface
area.

I chose = protein for calculation group
= protein for output group

what does it define hydrophobic solvent accessible surface area?
= does that, the surface area, enclose the hydrophobic atoms/residues?

what does it define hydrophilic solvent accessible surface area?
 = does that, the surface area, enclose the hydrophilic atoms/residues?


what does it define total solvent accessible surface area?
 = does that, the surface area, enclose the total surface of the protein?



I got hydrophobic SAS is  greater than hydrophilic SAS.
Isn't correct ?
I am supposing that hydrophobic atoms/residues are within the protein.
And, hydrophilic atoms/residues are on the surface of the protein.


Then, how can hydrophobic SAS is  greater than hydrophilic SAS ?

Thank you
Lin
-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php

[gmx-users] g_sas

2010-04-04 Thread Chih-Ying Lin

Hi
From David,
If you select a
group consisting of a single residue in a protein the SAS will be
computed as if the rest of the protein is not there. Very useful when
you want to compute protein-protein interface areas.


= therefore, if i select a group consisting of a single residue, which is
in the core of a protein, it is impossible that water penetrates into the
core of the protein so SAS is supposed to be zero.

= However, after calculation with g_sas, the SAS_calculation of the single
residue residing in the core of the protein is NOT ZERO.

= My understanding is that g_sas returns the surface area of the single
residue and it does not matter where the single residue locates.
 right?

= The single residue can locate in the core of the protein or on the
surface of the protein. The g_sas calculation for the single residue will
not make a huge difference unless the single residue deforms/ twists .
 on the surface or in the core of the protein,right ?


= How to compute protein-protein interface area?

= In the protein + ligands + water system, I want to compute protein-ligand
interface, protein-water interface, and ligand-water interface separately.
 = How?


= in the protein + water system, g_sas computes the total SAS fluctuating
between   88  and  144  (angstrom_squares)
= does it make sense ?
= I don't think that protein will swell 50 % plus in the pure water.
= But why ??


= How to calculate the surface area of a micelle ?

Thank you
Lin


















 Hi
 The command
 g_sas = Select a group for calculation of surface and a group for output


 What is the difference between a group for calculation of surface
 and a group for output?

 Please consult the documentation. From g_sas -h:

 The program will ask for a group for the surface calculation and a
 group for the output. The calculation group should always consists of
 all the non-solvent atoms in the system. The output group can be the
 whole or part of the calculation group.

Actually this documentation is not correct.

The calculation group are those atoms taken into account in the
computation, whether or not they are solvent accessible. If you select a
group consisting of a single residue in a protein the SAS will be
computed as if the rest of the protein is not there. Very useful when
you want to compute protein-protein interface areas.

 -Justin

 Thank you
 Lin




--
David.
-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php

[gmx-users] g_sas

2010-04-03 Thread Chih-Ying Lin

Hi
The command
g_sas =
Select a group for calculation of surface and a group for output


What is the difference between a group for calculation of surface and a
group for output?
Thank you
Lin
-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php

Re: [gmx-users] g_sas

2010-04-03 Thread Justin A. Lemkul




Chih-Ying Lin wrote:


Hi
The command
g_sas = 
Select a group for calculation of surface and a group for output



What is the difference between a group for calculation of surface and 
a group for output?


Please consult the documentation.  From g_sas -h:

The program will ask for a group for the surface calculation and a group for 
the output. The calculation group should always consists of all the non-solvent 
atoms in the system. The output group can be the whole or part of the 
calculation group.


-Justin


Thank you
Lin



--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.

Can't post? Read http://www.gromacs.org/mailing_lists/users.php

Re: [gmx-users] g_sas

2010-04-03 Thread David van der Spoel


On 4/3/10 8:36 PM, Justin A. Lemkul wrote:



Chih-Ying Lin wrote:


Hi
The command
g_sas = Select a group for calculation of surface and a group for output


What is the difference between a group for calculation of surface
and a group for output?


Please consult the documentation. From g_sas -h:

The program will ask for a group for the surface calculation and a
group for the output. The calculation group should always consists of
all the non-solvent atoms in the system. The output group can be the
whole or part of the calculation group.


Actually this documentation is not correct.

The calculation group are those atoms taken into account in the 
computation, whether or not they are solvent accessible. If you select a 
group consisting of a single residue in a protein the SAS will be 
computed as if the rest of the protein is not there. Very useful when 
you want to compute protein-protein interface areas.



-Justin


Thank you
Lin






--
David.

David van der Spoel, PhD, Professor of Biology
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  75124 Uppsala, Sweden
phone:  46 18 471 4205  fax: 46 18 511 755
sp...@xray.bmc.uu.sesp...@gromacs.org   http://folding.bmc.uu.se

--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.

Can't post? Read http://www.gromacs.org/mailing_lists/users.php

[gmx-users] g_sas

2010-04-03 Thread Chih-Ying Lin

HI
THe command =
g_sas_mpi -f 6LYZ-MD566500.xtc -s 6LYZ-MD566500.tpr -o
solvent-accessible-surface.xvg -oa atomic-sas.xvg -or residue-sas.xvg



In the solvent-accessible-surface.xvg =
@ s0 legend Hydrophobic
@ s1 legend Hydrophilic
@ s2 legend Total
@ s3 legend D Gsolv

What does Hydrophobic mean here?
What does Hydrophilic mean here?
Does Total = Hydrophobic+Hydrophilic ?
What does D Gsolv mean here?
How can Gromacs define Hydrophobic atoms and Hydrophilic atoms ?



What does the Area unit mean ? =  Area (nm\S2\N)


Thank you
Lin
-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php

[gmx-users] g_sas

2010-02-28 Thread pawan raghav

*I executed the following command.
**
**g_sas -s mdrun.tpr -f mdrun.trr -or mdrun.xvg
***
**
*xmgrace -nxy mdrun.xvg*

*I get two sets of values: one is bigger (black) than the other (red).
***
*I have checked the manual and other sources, but I could not find an
**answer about the black and red line.  If it was written in fine print and
I missed it, I am sorry
**about that. So I want to know is the red lower value, the standard error
or standard deviation or
something else? What does red and black line shows also link the reference.*
-- 
Pawan
-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php

Re: [gmx-users] g_sas

2010-02-28 Thread Tsjerk Wassenaar

Hi Pawan,

The legends are contained in the .xvg file. Try viewing the file.

Cheers,

Tsjerk

On Mon, Mar 1, 2010 at 8:29 AM, pawan raghav pwnr...@gmail.com wrote:
 I executed the following command.

 g_sas -s mdrun.tpr -f mdrun.trr -or mdrun.xvg

 xmgrace -nxy mdrun.xvg

 I get two sets of values: one is bigger (black) than the other (red).
 I have checked the manual and other sources, but I could not find an
 answer about the black and red line.  If it was written in fine print and I
 missed it, I am sorry
 about that. So I want to know is the red lower value, the standard error or
 standard deviation or
 something else? What does red and black line shows also link the reference.
 --
 Pawan
 --
 gmx-users mailing list    gmx-us...@gromacs.org
 http://lists.gromacs.org/mailman/listinfo/gmx-users
 Please search the archive at http://www.gromacs.org/search before posting!
 Please don't post (un)subscribe requests to the list. Use the
 www interface or send it to gmx-users-requ...@gromacs.org.
 Can't post? Read http://www.gromacs.org/mailing_lists/users.php




-- 
Tsjerk A. Wassenaar, Ph.D.

Computational Chemist
Medicinal Chemist
Neuropharmacologist
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php

Re: [gmx-users] g_sas

2010-02-28 Thread Mark Abraham


On 1/03/2010 6:29 PM, pawan raghav wrote:

/I executed the following command.
//
//g_sas -s mdrun.tpr -f mdrun.trr -or mdrun.xvg
///
//
/xmgrace -nxy mdrun.xvg/
/I get two sets of values: one is bigger (black) than the other (red).
///
/I have checked the manual and other sources, but I could not find an
//answer about the black and red line.  If it was written in fine print
and I missed it, I am sorry
//about that. So I want to know is the red lower value, the standard
error or standard deviation or
/something else? What does red and black line shows also link the
reference.//


Look in the .xvg file for the headings for the data sets s0, s1, etc.

Mark
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.

Can't post? Read http://www.gromacs.org/mailing_lists/users.php

[gmx-users] g_sas with pbc

2009-11-03 Thread andrea carotti

Hi all,
I've already simulated 27 organic molecules in a cubic solvent box. Now
I would like to calculate the SAS of this system. I've a tpr and a trr
with only the molecules inside (without water).
I'm using gromacs 4.0.5.
I've added the box dimension infos to the trr using the command:
trjconv -f ../../original_multi3000.pdb -o new.trr -s reference.pdb -box
7.3973   7.3973   7.3973
In the reference.pdb  I've also the CRYST informations.
I've modified the gmx_sas.c to bypass the check that turn off
automatically the PBC if solvent molecules are not present.
Unfortunately I've seen that the results with and without taking into
account the PBC are identical.
So my questions are:
1) Is it possible to use the g_sas tool to calculate the SAS of this
kind of system?
2) There are some tricks or trasformations or missing informations in my
input(s) that I could fill before running the analysis?
3)Should I use another type of box? Trasform the trajectory with some
pbc keywords (I've also tried -ur compact without luck)...

Thanks in advance and sorry for the long message
Andrea




___
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php

Re: [gmx-users] g_sas with pbc

2009-11-03 Thread David van der Spoel


andrea carotti wrote:

Hi all,
I've already simulated 27 organic molecules in a cubic solvent box. Now
I would like to calculate the SAS of this system. I've a tpr and a trr
with only the molecules inside (without water).
I'm using gromacs 4.0.5.
I've added the box dimension infos to the trr using the command:
trjconv -f ../../original_multi3000.pdb -o new.trr -s reference.pdb -box
7.3973   7.3973   7.3973
In the reference.pdb  I've also the CRYST informations.
I've modified the gmx_sas.c to bypass the check that turn off
automatically the PBC if solvent molecules are not present.
Unfortunately I've seen that the results with and without taking into
account the PBC are identical.
So my questions are:
1) Is it possible to use the g_sas tool to calculate the SAS of this
kind of system?
2) There are some tricks or trasformations or missing informations in my
input(s) that I could fill before running the analysis?
3)Should I use another type of box? Trasform the trajectory with some
pbc keywords (I've also tried -ur compact without luck)...

Thanks in advance and sorry for the long message
Andrea

There is an open bugzilla on this

http://bugzilla.gromacs.org/show_bug.cgi?id=197

In principle it should work, but there may still be a small bug. Feel 
free to upload a test system to this bugzilla.







___
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.

Can't post? Read http://www.gromacs.org/mailing_lists/users.php



--
David van der Spoel, Ph.D., Professor of Biology
Molec. Biophys. group, Dept. of Cell  Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205. Fax: +4618511755.
sp...@xray.bmc.uu.sesp...@gromacs.org   http://folding.bmc.uu.se
___
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.

Can't post? Read http://www.gromacs.org/mailing_lists/users.php

[gmx-users] g_sas

2009-07-08 Thread Smolin, Nikolai

Hi Gromacs user,

I need to calculate solvent accessible area for some water molecules.
I am wondering if g_sas can do it correctly. Do I need just define
surface group as : protein + water molecule?

Thanks,
Nikolai.
___
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php

Re: [gmx-users] g_sas

2009-04-23 Thread Justin A. Lemkul




Cheong Wee Loong, Daniel wrote:

Dear all,

 

I am interested to calculate the hydrophobic and hydrophilic area of the 
surface of the protein layer I am simulating.  It looked like g_sas 
would be able to give me what I was looking for.  But I was wondering 
what the difference is between the calculation group and the output 
group.  In particular, what is the output group?  I tried looking in the 
manual and in the archives but I can’t seem to find an answer to it. 



From g_sas -h:

The calculation group should always consists of all the non-solvent atoms in 
the system. The output group can be the whole or part of the calculation group.


-Justin

 


Thanks.



This email is confidential and may be privileged. If you are not the 
intended recipient, please delete it and notify us immediately. Please 
do not copy or use it for any purpose, or disclose its contents to any 
other person. Thank you.





___
gmx-users mailing listgmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.

Can't post? Read http://www.gromacs.org/mailing_lists/users.php


--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


___
gmx-users mailing listgmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php

RE: [gmx-users] g_sas

2009-04-23 Thread Cheong Wee Loong, Daniel

Thanks Justin for the reply.  I did read the help and manual and understand 
that the output file can be the whole or part of the calculation group.  What I 
don't quite understand is what the output group represents. I am assuming that 
the calculation group would be the group of atoms that will be probed to 
determine the solvent accessible are.  If so, what does the output group 
represent?

Thanks.


-Original Message-
From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On 
Behalf Of Justin A. Lemkul
Sent: Thursday, April 23, 2009 6:26 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] g_sas



Cheong Wee Loong, Daniel wrote:
 Dear all,



 I am interested to calculate the hydrophobic and hydrophilic area of the
 surface of the protein layer I am simulating.  It looked like g_sas
 would be able to give me what I was looking for.  But I was wondering
 what the difference is between the calculation group and the output
 group.  In particular, what is the output group?  I tried looking in the
 manual and in the archives but I can't seem to find an answer to it.


 From g_sas -h:

The calculation group should always consists of all the non-solvent atoms in
the system. The output group can be the whole or part of the calculation group.

-Justin



 Thanks.


 
 This email is confidential and may be privileged. If you are not the
 intended recipient, please delete it and notify us immediately. Please
 do not copy or use it for any purpose, or disclose its contents to any
 other person. Thank you.


 

 ___
 gmx-users mailing listgmx-users@gromacs.org
 http://www.gromacs.org/mailman/listinfo/gmx-users
 Please search the archive at http://www.gromacs.org/search before posting!
 Please don't post (un)subscribe requests to the list. Use the
 www interface or send it to gmx-users-requ...@gromacs.org.
 Can't post? Read http://www.gromacs.org/mailing_lists/users.php

--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


___
gmx-users mailing listgmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php

This email is confidential and may be privileged. If you are not the intended 
recipient, please delete it and notify us immediately. Please do not copy or 
use it for any purpose, or disclose its contents to any other person. Thank you.
___
gmx-users mailing listgmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php

Re: [gmx-users] g_sas

2009-04-23 Thread Justin A. Lemkul




Cheong Wee Loong, Daniel wrote:

Thanks Justin for the reply.  I did read the help and manual and understand
that the output file can be the whole or part of the calculation group.  What
I don't quite understand is what the output group represents. I am assuming
that the calculation group would be the group of atoms that will be probed to
determine the solvent accessible are.  If so, what does the output group
represent?



Consider the following situation.  I have a protein complex of protein A and 
protein B in explicit solvent with ions.  The calculation group includes 
everything that is non-solvent.  Now let's say I only care about the SASA of 
protein A.  Therefore, protein A is my output group, and I get hydrophilic, 
hydrophobic, and total SASA for protein A.  I can similarly run the calculation 
(with the same non-solvent calculation group) and output the SASA of protein B. 
 This is useful in that if the same calculation and output group is used, then 
some of the detail of (in my example) the protein complex may be lost.


For an aqueous protein, this point is pretty moot, but the selectable output 
group is a feature of most Gromacs tools to allow the user flexibility and 
versatility.


-Justin


Thanks.


-Original Message- From: gmx-users-boun...@gromacs.org
[mailto:gmx-users-boun...@gromacs.org] On Behalf Of Justin A. Lemkul Sent:
Thursday, April 23, 2009 6:26 PM To: Discussion list for GROMACS users 
Subject: Re: [gmx-users] g_sas




Cheong Wee Loong, Daniel wrote:

Dear all,



I am interested to calculate the hydrophobic and hydrophilic area of the 
surface of the protein layer I am simulating.  It looked like g_sas would

be able to give me what I was looking for.  But I was wondering what the
difference is between the calculation group and the output group.  In
particular, what is the output group?  I tried looking in the manual and in
the archives but I can't seem to find an answer to it.



From g_sas -h:

The calculation group should always consists of all the non-solvent atoms in
 the system. The output group can be the whole or part of the calculation
group.

-Justin



Thanks.


 
This email is confidential and may be privileged. If you are not the 
intended recipient, please delete it and notify us immediately. Please do

not copy or use it for any purpose, or disclose its contents to any other
person. Thank you.




___ gmx-users mailing list
gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 
Please search the archive at http://www.gromacs.org/search before posting! 
Please don't post (un)subscribe requests to the list. Use the www interface

or send it to gmx-users-requ...@gromacs.org. Can't post? Read
http://www.gromacs.org/mailing_lists/users.php


-- 

Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar Department of
Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080
 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

 
___ gmx-users mailing list
gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 
Please search the archive at http://www.gromacs.org/search before posting! 
Please don't post (un)subscribe requests to the list. Use the www interface

or send it to gmx-users-requ...@gromacs.org. Can't post? Read
http://www.gromacs.org/mailing_lists/users.php

This email is confidential and may be privileged. If you are not the intended
recipient, please delete it and notify us immediately. Please do not copy or
use it for any purpose, or disclose its contents to any other person. Thank
you.



--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


___
gmx-users mailing listgmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.

Can't post? Read http://www.gromacs.org/mailing_lists/users.php

RE: [gmx-users] g_sas

2009-04-23 Thread Cheong Wee Loong, Daniel

Thanks for the explanation.  It is much clearer now.  Although I still don't 
quite understand why we can't just use Protein A as the calculation group AND 
output group to find the SASA of protein A.  I know it states that the 
calculation group should be all non-solvent atoms, but I guess I am just trying 
to understand why.  As in why do we need both the calculation and output groups 
in the first place?  Why can't we just use the group of atoms that we are want 
to find the SASA for?



-Original Message-
From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On 
Behalf Of Justin A. Lemkul
Sent: Friday, April 24, 2009 10:17 AM
To: Gromacs Users' List
Subject: Re: [gmx-users] g_sas



Cheong Wee Loong, Daniel wrote:
 Thanks Justin for the reply.  I did read the help and manual and understand
 that the output file can be the whole or part of the calculation group.  What
 I don't quite understand is what the output group represents. I am assuming
 that the calculation group would be the group of atoms that will be probed to
 determine the solvent accessible are.  If so, what does the output group
 represent?


Consider the following situation.  I have a protein complex of protein A and
protein B in explicit solvent with ions.  The calculation group includes
everything that is non-solvent.  Now let's say I only care about the SASA of
protein A.  Therefore, protein A is my output group, and I get hydrophilic,
hydrophobic, and total SASA for protein A.  I can similarly run the calculation
(with the same non-solvent calculation group) and output the SASA of protein B.
  This is useful in that if the same calculation and output group is used, then
some of the detail of (in my example) the protein complex may be lost.

For an aqueous protein, this point is pretty moot, but the selectable output
group is a feature of most Gromacs tools to allow the user flexibility and
versatility.

-Justin

 Thanks.


 -Original Message- From: gmx-users-boun...@gromacs.org
 [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Justin A. Lemkul Sent:
 Thursday, April 23, 2009 6:26 PM To: Discussion list for GROMACS users
 Subject: Re: [gmx-users] g_sas



 Cheong Wee Loong, Daniel wrote:
 Dear all,



 I am interested to calculate the hydrophobic and hydrophilic area of the
 surface of the protein layer I am simulating.  It looked like g_sas would
 be able to give me what I was looking for.  But I was wondering what the
 difference is between the calculation group and the output group.  In
 particular, what is the output group?  I tried looking in the manual and in
 the archives but I can't seem to find an answer to it.


 From g_sas -h:

 The calculation group should always consists of all the non-solvent atoms in
  the system. The output group can be the whole or part of the calculation
 group.

 -Justin


 Thanks.


 
 This email is confidential and may be privileged. If you are not the
 intended recipient, please delete it and notify us immediately. Please do
 not copy or use it for any purpose, or disclose its contents to any other
 person. Thank you.


 

 ___ gmx-users mailing list
 gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users
 Please search the archive at http://www.gromacs.org/search before posting!
 Please don't post (un)subscribe requests to the list. Use the www interface
 or send it to gmx-users-requ...@gromacs.org. Can't post? Read
 http://www.gromacs.org/mailing_lists/users.php

 -- 

 Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar Department of
 Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080
  http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

 
 ___ gmx-users mailing list
 gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users
 Please search the archive at http://www.gromacs.org/search before posting!
 Please don't post (un)subscribe requests to the list. Use the www interface
 or send it to gmx-users-requ...@gromacs.org. Can't post? Read
 http://www.gromacs.org/mailing_lists/users.php

 This email is confidential and may be privileged. If you are not the intended
 recipient, please delete it and notify us immediately. Please do not copy or
 use it for any purpose, or disclose its contents to any other person. Thank
 you.


--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


___
gmx-users mailing list

Re: [gmx-users] g_sas

2009-04-23 Thread Justin A. Lemkul




Cheong Wee Loong, Daniel wrote:

Thanks for the explanation.  It is much clearer now.  Although I still don't
quite understand why we can't just use Protein A as the calculation group AND
output group to find the SASA of protein A.  I know it states that the
calculation group should be all non-solvent atoms, but I guess I am just
trying to understand why.  As in why do we need both the calculation and
output groups in the first place?  Why can't we just use the group of atoms
that we are want to find the SASA for?




That information is probably contained in the references that g_sas asks you to 
read and cite.


-Justin



-Original Message- From: gmx-users-boun...@gromacs.org
[mailto:gmx-users-boun...@gromacs.org] On Behalf Of Justin A. Lemkul Sent:
Friday, April 24, 2009 10:17 AM To: Gromacs Users' List Subject: Re:
[gmx-users] g_sas



Cheong Wee Loong, Daniel wrote:

Thanks Justin for the reply.  I did read the help and manual and understand
 that the output file can be the whole or part of the calculation group.
What I don't quite understand is what the output group represents. I am
assuming that the calculation group would be the group of atoms that will
be probed to determine the solvent accessible are.  If so, what does the
output group represent?



Consider the following situation.  I have a protein complex of protein A and 
protein B in explicit solvent with ions.  The calculation group includes 
everything that is non-solvent.  Now let's say I only care about the SASA of 
protein A.  Therefore, protein A is my output group, and I get hydrophilic, 
hydrophobic, and total SASA for protein A.  I can similarly run the

calculation (with the same non-solvent calculation group) and output the SASA
of protein B. This is useful in that if the same calculation and output group
is used, then some of the detail of (in my example) the protein complex may
be lost.

For an aqueous protein, this point is pretty moot, but the selectable output 
group is a feature of most Gromacs tools to allow the user flexibility and 
versatility.


-Justin


Thanks.


-Original Message- From: gmx-users-boun...@gromacs.org 
[mailto:gmx-users-boun...@gromacs.org] On Behalf Of Justin A. Lemkul Sent: 
Thursday, April 23, 2009 6:26 PM To: Discussion list for GROMACS users 
Subject: Re: [gmx-users] g_sas




Cheong Wee Loong, Daniel wrote:

Dear all,



I am interested to calculate the hydrophobic and hydrophilic area of the 
surface of the protein layer I am simulating.  It looked like g_sas would

 be able to give me what I was looking for.  But I was wondering what the
 difference is between the calculation group and the output group.  In 
particular, what is the output group?  I tried looking in the manual and

in the archives but I can't seem to find an answer to it.


From g_sas -h:

The calculation group should always consists of all the non-solvent atoms
in the system. The output group can be the whole or part of the calculation
 group.

-Justin


Thanks.


 
This email is confidential and may be privileged. If you are not the 
intended recipient, please delete it and notify us immediately. Please do

 not copy or use it for any purpose, or disclose its contents to any
other person. Thank you.




___ gmx-users mailing list 
gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 
Please search the archive at http://www.gromacs.org/search before

posting! Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org. Can't post?
Read http://www.gromacs.org/mailing_lists/users.php

-- 

Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar Department of 
Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540)

231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

 
___ gmx-users mailing list 
gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 
Please search the archive at http://www.gromacs.org/search before posting! 
Please don't post (un)subscribe requests to the list. Use the www interface
 or send it to gmx-users-requ...@gromacs.org. Can't post? Read 
http://www.gromacs.org/mailing_lists/users.php


This email is confidential and may be privileged. If you are not the
intended recipient, please delete it and notify us immediately. Please do
not copy or use it for any purpose, or disclose its contents to any other
person. Thank you.



-- 

Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar Department of
Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080
 http://www.bevanlab.biochem.vt.edu/Pages

RE: [gmx-users] g_sas

2009-04-23 Thread Cheong Wee Loong, Daniel

Ah ok. Fair enough.  Thanks!

-Original Message-
From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On 
Behalf Of Justin A. Lemkul
Sent: Friday, April 24, 2009 10:48 AM
To: Gromacs Users' List
Subject: Re: [gmx-users] g_sas

Cheong Wee Loong, Daniel wrote:
 Thanks for the explanation.  It is much clearer now.  Although I still don't
 quite understand why we can't just use Protein A as the calculation group AND
 output group to find the SASA of protein A.  I know it states that the
 calculation group should be all non-solvent atoms, but I guess I am just
 trying to understand why.  As in why do we need both the calculation and
 output groups in the first place?  Why can't we just use the group of atoms
 that we are want to find the SASA for?

That information is probably contained in the references that g_sas asks you to
read and cite.

-Justin

 -Original Message- From: gmx-users-boun...@gromacs.org
 [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Justin A. Lemkul Sent:
 Friday, April 24, 2009 10:17 AM To: Gromacs Users' List Subject: Re:
 [gmx-users] g_sas

 Cheong Wee Loong, Daniel wrote:
 Thanks Justin for the reply.  I did read the help and manual and understand
  that the output file can be the whole or part of the calculation group.
 What I don't quite understand is what the output group represents. I am
 assuming that the calculation group would be the group of atoms that will
 be probed to determine the solvent accessible are.  If so, what does the
 output group represent?

 Consider the following situation.  I have a protein complex of protein A and
 protein B in explicit solvent with ions.  The calculation group includes
 everything that is non-solvent.  Now let's say I only care about the SASA of
 protein A.  Therefore, protein A is my output group, and I get hydrophilic,
 hydrophobic, and total SASA for protein A.  I can similarly run the
 calculation (with the same non-solvent calculation group) and output the SASA
 of protein B. This is useful in that if the same calculation and output group
 is used, then some of the detail of (in my example) the protein complex may
 be lost.

 For an aqueous protein, this point is pretty moot, but the selectable output
 group is a feature of most Gromacs tools to allow the user flexibility and
 versatility.

 -Justin

 Thanks.

 -Original Message- From: gmx-users-boun...@gromacs.org
 [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Justin A. Lemkul Sent:
 Thursday, April 23, 2009 6:26 PM To: Discussion list for GROMACS users
 Subject: Re: [gmx-users] g_sas

 Cheong Wee Loong, Daniel wrote:
 Dear all,

 I am interested to calculate the hydrophobic and hydrophilic area of the
 surface of the protein layer I am simulating.  It looked like g_sas would
  be able to give me what I was looking for.  But I was wondering what the
  difference is between the calculation group and the output group.  In
 particular, what is the output group?  I tried looking in the manual and
 in the archives but I can't seem to find an answer to it.

 From g_sas -h:

 The calculation group should always consists of all the non-solvent atoms
 in the system. The output group can be the whole or part of the calculation
  group.

 -Justin

 Thanks.

 This email is confidential and may be privileged. If you are not the
 intended recipient, please delete it and notify us immediately. Please do
  not copy or use it for any purpose, or disclose its contents to any
 other person. Thank you.

 ___ gmx-users mailing list
 gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users
 Please search the archive at http://www.gromacs.org/search before
 posting! Please don't post (un)subscribe requests to the list. Use the
 www interface or send it to gmx-users-requ...@gromacs.org. Can't post?
 Read http://www.gromacs.org/mailing_lists/users.php
 -- 

 Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar Department of
 Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540)
 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

 ___ gmx-users mailing list
 gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users
 Please search the archive at http://www.gromacs.org/search before posting!
 Please don't post (un)subscribe requests to the list. Use the www interface
  or send it to gmx-users-requ...@gromacs.org. Can't post? Read
 http://www.gromacs.org/mailing_lists/users.php

 This email is confidential and may be privileged. If you are not the
 intended recipient, please delete it and notify us immediately. Please do
 not copy or use it for any purpose

Re: [gmx-users] g_sas

2009-04-23 Thread Tsjerk Wassenaar

Hi,

Of course you can. But if part of Protein A is buried in an interface,
doing the SAS calculation over A only will also include the surface
interface; it will give the total surface of A. That may actually be
handy if you want to determine what the buried surface is. You
calculate the total surface for protein A and the total surface for
A+B. In both cases you use Protein A for the output. Then subtracting
one from the other gives the buried surface area. So it makes sense
calculating the area over Protein A, but it's just something
different.

Hope it's clear.

Cheers,

Tsjerk


On Fri, Apr 24, 2009 at 4:48 AM, Justin A. Lemkul jalem...@vt.edu wrote:


 Cheong Wee Loong, Daniel wrote:

 Thanks for the explanation.  It is much clearer now.  Although I still
 don't
 quite understand why we can't just use Protein A as the calculation group
 AND
 output group to find the SASA of protein A.  I know it states that the
 calculation group should be all non-solvent atoms, but I guess I am just
 trying to understand why.  As in why do we need both the calculation and
 output groups in the first place?  Why can't we just use the group of
 atoms
 that we are want to find the SASA for?



 That information is probably contained in the references that g_sas asks you
 to read and cite.

 -Justin


 -Original Message- From: gmx-users-boun...@gromacs.org
 [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Justin A. Lemkul Sent:
 Friday, April 24, 2009 10:17 AM To: Gromacs Users' List Subject: Re:
 [gmx-users] g_sas



 Cheong Wee Loong, Daniel wrote:

 Thanks Justin for the reply.  I did read the help and manual and
 understand
  that the output file can be the whole or part of the calculation group.
 What I don't quite understand is what the output group represents. I am
 assuming that the calculation group would be the group of atoms that will
 be probed to determine the solvent accessible are.  If so, what does the
 output group represent?


 Consider the following situation.  I have a protein complex of protein A
 and protein B in explicit solvent with ions.  The calculation group includes
 everything that is non-solvent.  Now let's say I only care about the SASA of
 protein A.  Therefore, protein A is my output group, and I get hydrophilic,
 hydrophobic, and total SASA for protein A.  I can similarly run the
 calculation (with the same non-solvent calculation group) and output the
 SASA
 of protein B. This is useful in that if the same calculation and output
 group
 is used, then some of the detail of (in my example) the protein complex
 may
 be lost.

 For an aqueous protein, this point is pretty moot, but the selectable
 output group is a feature of most Gromacs tools to allow the user
 flexibility and versatility.

 -Justin

 Thanks.


 -Original Message- From: gmx-users-boun...@gromacs.org
 [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Justin A. Lemkul Sent:
 Thursday, April 23, 2009 6:26 PM To: Discussion list for GROMACS users
 Subject: Re: [gmx-users] g_sas



 Cheong Wee Loong, Daniel wrote:

 Dear all,



 I am interested to calculate the hydrophobic and hydrophilic area of the
 surface of the protein layer I am simulating.  It looked like g_sas would
  be able to give me what I was looking for.  But I was wondering what
 the
  difference is between the calculation group and the output group.  In
 particular, what is the output group?  I tried looking in the manual and
 in the archives but I can't seem to find an answer to it.

 From g_sas -h:

 The calculation group should always consists of all the non-solvent
 atoms
 in the system. The output group can be the whole or part of the
 calculation
  group.

 -Justin

 Thanks.


 
 This email is confidential and may be privileged. If you are not the
 intended recipient, please delete it and notify us immediately. Please do
  not copy or use it for any purpose, or disclose its contents to any
 other person. Thank you.


 

 ___ gmx-users mailing list
 gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users
 Please search the archive at http://www.gromacs.org/search before
 posting! Please don't post (un)subscribe requests to the list. Use the
 www interface or send it to gmx-users-requ...@gromacs.org. Can't post?
 Read http://www.gromacs.org/mailing_lists/users.php

 -- 

 Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar Department of
 Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540)
 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

 
 ___ gmx-users mailing list
 gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users
 Please search the archive at http

RE: [gmx-users] g_sas

2009-04-23 Thread Cheong Wee Loong, Daniel

Hi all.  Thanks for all your replies.  I think I understand it now and can 
definitely see how having the calculation and output group would add to the 
flexibility and utilty of g_sas.

Thanks.

Daniel



-Original Message-
From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On 
Behalf Of Tsjerk Wassenaar
Sent: Friday, April 24, 2009 1:30 PM
To: jalem...@vt.edu; Discussion list for GROMACS users
Subject: Re: [gmx-users] g_sas

Hi,

Of course you can. But if part of Protein A is buried in an interface,
doing the SAS calculation over A only will also include the surface
interface; it will give the total surface of A. That may actually be
handy if you want to determine what the buried surface is. You
calculate the total surface for protein A and the total surface for
A+B. In both cases you use Protein A for the output. Then subtracting
one from the other gives the buried surface area. So it makes sense
calculating the area over Protein A, but it's just something
different.

Hope it's clear.

Cheers,

Tsjerk


On Fri, Apr 24, 2009 at 4:48 AM, Justin A. Lemkul jalem...@vt.edu wrote:


 Cheong Wee Loong, Daniel wrote:

 Thanks for the explanation.  It is much clearer now.  Although I still
 don't
 quite understand why we can't just use Protein A as the calculation group
 AND
 output group to find the SASA of protein A.  I know it states that the
 calculation group should be all non-solvent atoms, but I guess I am just
 trying to understand why.  As in why do we need both the calculation and
 output groups in the first place?  Why can't we just use the group of
 atoms
 that we are want to find the SASA for?



 That information is probably contained in the references that g_sas asks you
 to read and cite.

 -Justin


 -Original Message- From: gmx-users-boun...@gromacs.org
 [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Justin A. Lemkul Sent:
 Friday, April 24, 2009 10:17 AM To: Gromacs Users' List Subject: Re:
 [gmx-users] g_sas



 Cheong Wee Loong, Daniel wrote:

 Thanks Justin for the reply.  I did read the help and manual and
 understand
  that the output file can be the whole or part of the calculation group.
 What I don't quite understand is what the output group represents. I am
 assuming that the calculation group would be the group of atoms that will
 be probed to determine the solvent accessible are.  If so, what does the
 output group represent?


 Consider the following situation.  I have a protein complex of protein A
 and protein B in explicit solvent with ions.  The calculation group includes
 everything that is non-solvent.  Now let's say I only care about the SASA of
 protein A.  Therefore, protein A is my output group, and I get hydrophilic,
 hydrophobic, and total SASA for protein A.  I can similarly run the
 calculation (with the same non-solvent calculation group) and output the
 SASA
 of protein B. This is useful in that if the same calculation and output
 group
 is used, then some of the detail of (in my example) the protein complex
 may
 be lost.

 For an aqueous protein, this point is pretty moot, but the selectable
 output group is a feature of most Gromacs tools to allow the user
 flexibility and versatility.

 -Justin

 Thanks.


 -Original Message- From: gmx-users-boun...@gromacs.org
 [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Justin A. Lemkul Sent:
 Thursday, April 23, 2009 6:26 PM To: Discussion list for GROMACS users
 Subject: Re: [gmx-users] g_sas



 Cheong Wee Loong, Daniel wrote:

 Dear all,



 I am interested to calculate the hydrophobic and hydrophilic area of the
 surface of the protein layer I am simulating.  It looked like g_sas would
  be able to give me what I was looking for.  But I was wondering what
 the
  difference is between the calculation group and the output group.  In
 particular, what is the output group?  I tried looking in the manual and
 in the archives but I can't seem to find an answer to it.

 From g_sas -h:

 The calculation group should always consists of all the non-solvent
 atoms
 in the system. The output group can be the whole or part of the
 calculation
  group.

 -Justin

 Thanks.


 
 This email is confidential and may be privileged. If you are not the
 intended recipient, please delete it and notify us immediately. Please do
  not copy or use it for any purpose, or disclose its contents to any
 other person. Thank you.


 

 ___ gmx-users mailing list
 gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users
 Please search the archive at http://www.gromacs.org/search before
 posting! Please don't post (un)subscribe requests to the list. Use the
 www interface or send it to gmx-users-requ...@gromacs.org. Can't post?
 Read http://www.gromacs.org/mailing_lists/users.php

Re: [gmx-users] g_sas, what's it all about?

2008-07-31 Thread Peyman Yamin

On Wednesday 30 July 2008 12:58, David van der Spoel wrote:
 Peyman Yamin wrote:
  Hello List!
 
  I use g_sas to calculate the solvent accessible surface area of some
  amphiphiles. g_sas gives the result as hydrophobic area! I'm wondering if
  the hydrophilic part is somehow not recognized, or these terms mean
  different things in g_sas context? For Triton, for instance, a big
  surface is hydrophilic, to my knowledge!

 xmgrace -nxy sas.xvg

Thanks David, but what about other question marks?!

What is hydrophilic area? is it the wetted or solvated or maybe area on which 
the solvent molecules are with less than a distance apart from surface, or 
something else? In Triton, the length of the part which is interacting in a 
hydrophilic way is bigger actually, but I see a result of g_sas telling me that 
hydrophobic area is ~50 times bigger!!


 I use ffG43a1. Is it a strange behavior to calculate SAS from a UA
 trajectory?
 I mean is the CHx groups' H size taken intro account ?
 
 
 How is the DGsolv calculated by g_sas? and the areas ? which algorithm?
 where is the code? reference?
 
 
 Is there any program with which one could calculate the volume enclosed
 by SAS resulted from g_sas? Just if one used such and can trust any code
 available anywhere??

 I see different posts in the mailing list addressing the accuracy of
 g_sas! Well, I'm using gmx 3.3.1; is the accompanying g_sas reliable?
 
 Any comment is truthfully appreciated :)
 
 Peyman
 
 
  P.S. Edmund Husserl believed, that we would indeed be in a nasty
  position, if empirical science were the only kind of science possible.

-- 
Peyman Yamin
Lehrstuhl fuer Thermische Verfahrenstechnik
Universitaet Erlangen-Nuernberg
Egerlandstr. 3
91058 Erlangen
Phone: +49(0) - 9131 - 85 27671
Mailto: [EMAIL PROTECTED]___
gmx-users mailing listgmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php

Re: [gmx-users] g_sas, what's it all about?

2008-07-31 Thread Justin A. Lemkul




Peyman Yamin wrote:

On Wednesday 30 July 2008 12:58, David van der Spoel wrote:


 Peyman Yamin wrote:



  Hello List!



 



  I use g_sas to calculate the solvent accessible surface area of some


  amphiphiles. g_sas gives the result as hydrophobic area! I'm 

wondering if


  the hydrophilic part is somehow not recognized, or these terms mean



  different things in g_sas context? For Triton, for instance, a big



  surface is hydrophilic, to my knowledge!







 xmgrace -nxy sas.xvg


Thanks David, but what about other question marks?!

What is hydrophilic area? is it the wetted or solvated or maybe area on 
which the solvent molecules are with less than a distance apart from 
surface, or something else? In Triton, the length of the part which is 
interacting in a hydrophilic way is bigger actually, but I see a result 
of g_sas telling me that hydrophobic area is ~50 times bigger!!




I believe g_sas decides hydrophobicity and hydrophilicity based on charge (and 
thus altered with the -qmax flag), from the description in the manual page.  I 
could be wrong, so someone please correct me if you are more familiar with the code.


I think you are thinking of the area somewhat backwards.  Just because part of 
the molecule is interacting with the solvent does not make it hydrophilic 
surface area.  Hence why you can have hydrophobic surface area - if, for 
example, an alkyl chain is protruding into bulk solution, it is actually 
hydrophobic, but accessible to solvent.


And, from what I understand, Triton is actually primarily hydrophobic, so a 50X 
greater hydrophobic surface area does not surprise me.



I use ffG43a1. Is it a strange behavior to calculate SAS from a UA

trajectory?



Not at all.  I have seen such analysis in the literature.


I mean is the CHx groups' H size taken intro account ?


 


How is the DGsolv calculated by g_sas? and the areas ? which algorithm?

where is the code? reference?



The code would be in g_sas.c, would be my guess.


 


Is there any program with which one could calculate the volume enclosed

by SAS resulted from g_sas? Just if one used such and can trust any code

available anywhere??


Volumes and densities can be printed with g_sas -tv, but I don't know if this is 
what you're after.


-Justin



I see different posts in the mailing list addressing the accuracy of

g_sas! Well, I'm using gmx 3.3.1; is the accompanying g_sas reliable?


 


Any comment is truthfully appreciated :)


 


Peyman


 



 



 P.S. Edmund Husserl believed, that we would indeed be in a nasty



 position, if empirical science were the only kind of science possible.


--

Peyman Yamin

Lehrstuhl fuer Thermische Verfahrenstechnik

Universitaet Erlangen-Nuernberg

Egerlandstr. 3

91058 Erlangen

Phone: +49(0) - 9131 - 85 27671

Mailto: [EMAIL PROTECTED]




___
gmx-users mailing listgmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to [EMAIL PROTECTED]

Can't post? Read http://www.gromacs.org/mailing_lists/users.php


--


Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


___
gmx-users mailing listgmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to [EMAIL PROTECTED]

Can't post? Read http://www.gromacs.org/mailing_lists/users.php

Re: [gmx-users] g_sas, what's it all about?

2008-07-31 Thread Peyman Yamin

On Thursday 31 July 2008 13:34, Justin A. Lemkul wrote:
 Peyman Yamin wrote:
  On Wednesday 30 July 2008 12:58, David van der Spoel wrote:
   Peyman Yamin wrote:
Hello List!
   
   
   
I use g_sas to calculate the solvent accessible surface area of some
   
amphiphiles. g_sas gives the result as hydrophobic area! I'm
 
  wondering if
 
the hydrophilic part is somehow not recognized, or these terms mean
   
different things in g_sas context? For Triton, for instance, a big
   
surface is hydrophilic, to my knowledge!
 
   xmgrace -nxy sas.xvg
 
  Thanks David, but what about other question marks?!
 
  What is hydrophilic area? is it the wetted or solvated or maybe area on
  which the solvent molecules are with less than a distance apart from
  surface, or something else? In Triton, the length of the part which is
  interacting in a hydrophilic way is bigger actually, but I see a result
  of g_sas telling me that hydrophobic area is ~50 times bigger!!

Hi Justin,
Thanks for the comments,

 I believe g_sas decides hydrophobicity and hydrophilicity based on charge
 (and thus altered with the -qmax flag), from the description in the manual
 page.  I could be wrong, so someone please correct me if you are more
 familiar with the code.

 I think you are thinking of the area somewhat backwards.  Just because part
 of the molecule is interacting with the solvent does not make it
 hydrophilic surface area.  Hence why you can have hydrophobic surface area
 - if, for example, an alkyl chain is protruding into bulk solution, it is
 actually hydrophobic, but accessible to solvent.


I think I said  interacting in a hydrophilic way and not just interacting. 
I completely agree with you on the fact that atoms could be accessible to the 
solvent and still be hydrophobic. In the end a vacuum in the solvent is not 
that desirable, I believe. But I more or less mean wettet in the context of 
Physical Chemistry, particularly D. Chandler (Nature|Vol 437|29 Sep 2005).

 And, from what I understand, Triton is actually primarily hydrophobic, so a
 50X greater hydrophobic surface area does not surprise me.

TritonX100 has a big head which consists of a chain of ...-CH2-O-CH2-O-... . 
This (C2H4O)n , n~10 is actually hydrophilic and is bigger than the 
hydrophobic tail of the surfactant which is a 
4-(1,1,3,3-tetramethylbutyl)-phenyl group. Based on this I expect the 
hydrophilic area should not be drastically smaller than the lipophilic part, 
as I get from g_sas. 

  I use ffG43a1. Is it a strange behavior to calculate SAS from a UA
 
  trajectory?

 Not at all.  I have seen such analysis in the literature.

  I mean is the CHx groups' H size taken intro account ?
 
 
 
  How is the DGsolv calculated by g_sas? and the areas ? which algorithm?
 
  where is the code? reference?

 The code would be in g_sas.c, would be my guess.

Have you - anyone else? -  by chance seen any literature refering to the 
algorithm used in g_sas??


  Is there any program with which one could calculate the volume enclosed
 
  by SAS resulted from g_sas? Just if one used such and can trust any code
 
  available anywhere??

 Volumes and densities can be printed with g_sas -tv, but I don't know if
 this is what you're after.

Well, this would be nice but I don't even have such a switch in my g_sas!!

---
Program g_sas, VERSION 3.3.1
Source code file: statutil.c, line: 799

Invalid command line argument:
-tv
---

Peyman



 -Justin

  I see different posts in the mailing list addressing the accuracy of
 
  g_sas! Well, I'm using gmx 3.3.1; is the accompanying g_sas reliable?
 
 
 
  Any comment is truthfully appreciated :)
 
 
 
  Peyman
 
   P.S. Edmund Husserl believed, that we would indeed be in a nasty
 
   position, if empirical science were the only kind of science possible.
 
  --
 
  Peyman Yamin
 
  Lehrstuhl fuer Thermische Verfahrenstechnik
 
  Universitaet Erlangen-Nuernberg
 
  Egerlandstr. 3
 
  91058 Erlangen
 
  Phone: +49(0) - 9131 - 85 27671
 
  Mailto: [EMAIL PROTECTED]
 
 
  
 
  ___
  gmx-users mailing listgmx-users@gromacs.org
  http://www.gromacs.org/mailman/listinfo/gmx-users
  Please search the archive at http://www.gromacs.org/search before
  posting! Please don't post (un)subscribe requests to the list. Use the
  www interface or send it to [EMAIL PROTECTED]
  Can't post? Read http://www.gromacs.org/mailing_lists/users.php

-- 
Peyman Yamin
Lehrstuhl fuer Thermische Verfahrenstechnik
Universitaet Erlangen-Nuernberg
Egerlandstr. 3
91058 Erlangen
Phone: +49(0) - 9131 - 85 27671
Mailto: [EMAIL PROTECTED]
___
gmx-users mailing listgmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at

Re: [gmx-users] g_sas, what's it all about?

2008-07-31 Thread Justin A. Lemkul




Peyman Yamin wrote:

On Thursday 31 July 2008 13:34, Justin A. Lemkul wrote:

Peyman Yamin wrote:

On Wednesday 30 July 2008 12:58, David van der Spoel wrote:

 Peyman Yamin wrote:
  Hello List!
 
 
 
  I use g_sas to calculate the solvent accessible surface area of some
 
  amphiphiles. g_sas gives the result as hydrophobic area! I'm

wondering if


  the hydrophilic part is somehow not recognized, or these terms mean
 
  different things in g_sas context? For Triton, for instance, a big
 
  surface is hydrophilic, to my knowledge!

 xmgrace -nxy sas.xvg

Thanks David, but what about other question marks?!

What is hydrophilic area? is it the wetted or solvated or maybe area on
which the solvent molecules are with less than a distance apart from
surface, or something else? In Triton, the length of the part which is
interacting in a hydrophilic way is bigger actually, but I see a result
of g_sas telling me that hydrophobic area is ~50 times bigger!!

Hi Justin,
Thanks for the comments,


I believe g_sas decides hydrophobicity and hydrophilicity based on charge
(and thus altered with the -qmax flag), from the description in the manual
page.  I could be wrong, so someone please correct me if you are more
familiar with the code.

I think you are thinking of the area somewhat backwards.  Just because part
of the molecule is interacting with the solvent does not make it
hydrophilic surface area.  Hence why you can have hydrophobic surface area
- if, for example, an alkyl chain is protruding into bulk solution, it is
actually hydrophobic, but accessible to solvent.



I think I said  interacting in a hydrophilic way and not just interacting. 
I completely agree with you on the fact that atoms could be accessible to the 
solvent and still be hydrophobic. In the end a vacuum in the solvent is not 
that desirable, I believe. But I more or less mean wettet in the context of 
Physical Chemistry, particularly D. Chandler (Nature|Vol 437|29 Sep 2005).



And, from what I understand, Triton is actually primarily hydrophobic, so a
50X greater hydrophobic surface area does not surprise me.

TritonX100 has a big head which consists of a chain of ...-CH2-O-CH2-O-... . 
This (C2H4O)n , n~10 is actually hydrophilic and is bigger than the 
hydrophobic tail of the surfactant which is a 
4-(1,1,3,3-tetramethylbutyl)-phenyl group. Based on this I expect the 
hydrophilic area should not be drastically smaller than the lipophilic part, 
as I get from g_sas. 


I guess, then, it would depend on the charges you have assigned (based on what I 
read about g_sas from the help info).  If you have parameterized these ether 
linkages such that they are more polar, than g_sas should detect them as such. 
Beyond that, I can't comment on it.





I use ffG43a1. Is it a strange behavior to calculate SAS from a UA

trajectory?

Not at all.  I have seen such analysis in the literature.


I mean is the CHx groups' H size taken intro account ?



How is the DGsolv calculated by g_sas? and the areas ? which algorithm?

where is the code? reference?

The code would be in g_sas.c, would be my guess.


Have you - anyone else? -  by chance seen any literature refering to the 
algorithm used in g_sas??


I would look for publications by Connolly.  I believe the algorithm derives from 
that work.





Is there any program with which one could calculate the volume enclosed

by SAS resulted from g_sas? Just if one used such and can trust any code

available anywhere??

Volumes and densities can be printed with g_sas -tv, but I don't know if
this is what you're after.


Well, this would be nice but I don't even have such a switch in my g_sas!!



Apologies :)  I have GMX 3.3.3, and without checking that you had 3.3.1, I was 
looking at my command line options.  Maybe upgrading would serve you well?


-Justin



---
Program g_sas, VERSION 3.3.1
Source code file: statutil.c, line: 799

Invalid command line argument:
-tv
---

Peyman



-Justin


I see different posts in the mailing list addressing the accuracy of

g_sas! Well, I'm using gmx 3.3.1; is the accompanying g_sas reliable?



Any comment is truthfully appreciated :)



Peyman


 P.S. Edmund Husserl believed, that we would indeed be in a nasty

 position, if empirical science were the only kind of science possible.

--

Peyman Yamin

Lehrstuhl fuer Thermische Verfahrenstechnik

Universitaet Erlangen-Nuernberg

Egerlandstr. 3

91058 Erlangen

Phone: +49(0) - 9131 - 85 27671

Mailto: [EMAIL PROTECTED]




___
gmx-users mailing listgmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before
posting! Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [EMAIL

Re: [gmx-users] g_sas, what's it all about?

2008-07-31 Thread Michel Cuendet



Hi list,

I wanted to post something about g_sas some time ago already, but didn't 
find time to. Here is the occasion.


I believe g_sas does not actually compute the solvent accessible surface 
area (SASA, defined as the locus of the center of the probe sphere), but 
rather the molecular surface (defined using the surface of the probe 
sphere). See


http://www.netsci.org/Science/Compchem/feature14e.html

This should really be explained in the help of g_sas, together with the 
references for the algorithm used. It would also be nice to have an 
option to calculate the true SASA, in addition to the molecular surface.


How is the DGsolv calculated by g_sas? and the areas ? which algorithm?

where is the code? reference?


The code would be in g_sas.c, would be my guess.

The reference is in the code.

 D. Eisenberg and A. D. McLachlan,
 Solvation energy in protein folding and binding,
 Nature,
 319, 1986, 199-203

This method is completely different from the way nonpolar solvation free 
energy is calculated in implicit solvation models such as GBSA, which is 
based on the true SASA. The method of Eisenberg seems more detailed 
though, because it attributes different weights to surface patches 
depending on the type of the underlying atom. It would be interesting to 
know why this method has not been more widely used.


Best,
Michel

--

==
Michel Cuendet, Ph.D
Molecular Modeling Group
Swiss Institute of Bioinformatics
CH-1015 Lausanne, Switzerland
http://ludwig-sun1.unil.ch/~mcuendet
==


___
gmx-users mailing listgmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to [EMAIL PROTECTED]

Can't post? Read http://www.gromacs.org/mailing_lists/users.php

Re: [gmx-users] g_sas, what's it all about?

2008-07-31 Thread David van der Spoel


Michel Cuendet wrote:


Hi list,

I wanted to post something about g_sas some time ago already, but didn't 
find time to. Here is the occasion.


I believe g_sas does not actually compute the solvent accessible surface 
area (SASA, defined as the locus of the center of the probe sphere), but 
rather the molecular surface (defined using the surface of the probe 
sphere). See


http://www.netsci.org/Science/Compchem/feature14e.html

This should really be explained in the help of g_sas, together with the 
references for the algorithm used. It would also be nice to have an 
option to calculate the true SASA, in addition to the molecular surface.


The reference to the algorithm is also printed when you run the program. 
The algorithm used gives basically the same result as the MSMS program 
from Scripps.




How is the DGsolv calculated by g_sas? and the areas ? which algorithm?

where is the code? reference?


The code would be in g_sas.c, would be my guess.

The reference is in the code.

 D. Eisenberg and A. D. McLachlan,
 Solvation energy in protein folding and binding,
 Nature,
 319, 1986, 199-203

This method is completely different from the way nonpolar solvation free 
energy is calculated in implicit solvation models such as GBSA, which is 
based on the true SASA. The method of Eisenberg seems more detailed 
though, because it attributes different weights to surface patches 
depending on the type of the underlying atom. It would be interesting to 
know why this method has not been more widely used.


This free energy estimate is close to useless, but easy to compute.
When using Amber atom types it would also be possible to use a slightly 
more modern variant (JPCB 105 (2001) 5055), which is not necessarily a 
lot better though.




Best,
Michel




--
David van der Spoel, Ph.D., Professor of Biology
Molec. Biophys. group, Dept. of Cell  Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205. Fax: +4618511755.
[EMAIL PROTECTED]   [EMAIL PROTECTED]   http://folding.bmc.uu.se
___
gmx-users mailing listgmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to [EMAIL PROTECTED]

Can't post? Read http://www.gromacs.org/mailing_lists/users.php

[gmx-users] g_sas, what's it all about?

2008-07-30 Thread Peyman Yamin

Hello List!

I use g_sas to calculate the solvent accessible surface area of some 
amphiphiles. g_sas gives the result as hydrophobic area! I'm wondering if the 
hydrophilic part is somehow not recognized, or these terms mean different 
things in g_sas context? For Triton, for instance, a big surface is 
hydrophilic, to my knowledge!

I use ffG43a1. Is it a strange behavior to calculate SAS from a UA trajectory? 

How is the DGsolv calculated by g_sas? and the areas ? which algorithm? where 
is the code?

Is there any program with which one could calculate the volume enclosed by SAS 
resulted from g_sas?

I see different posts in the mailing list addressing the accuracy of g_sas! 
Well, I'm using gmx 3.3.1; is the accompanying g_sas reliable?

Any comment is truthfully appreciated :)

Peyman


P.S. Edmund Husserl believed, that we would indeed be in a nasty position, if 
empirical science were the only kind of science possible. 
-- 
Peyman Yamin
Lehrstuhl fuer Thermische Verfahrenstechnik
Universitaet Erlangen-Nuernberg
Egerlandstr. 3
91058 Erlangen
Phone: +49(0) - 9131 - 85 27671
Mailto: [EMAIL PROTECTED]
___
gmx-users mailing listgmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php

Re: [gmx-users] g_sas, what's it all about?

2008-07-30 Thread David van der Spoel


Peyman Yamin wrote:

Hello List!

I use g_sas to calculate the solvent accessible surface area of some 
amphiphiles. g_sas gives the result as hydrophobic area! I'm wondering if the 
hydrophilic part is somehow not recognized, or these terms mean different 
things in g_sas context? For Triton, for instance, a big surface is 
hydrophilic, to my knowledge!

xmgrace -nxy sas.xvg



I use ffG43a1. Is it a strange behavior to calculate SAS from a UA trajectory? 

How is the DGsolv calculated by g_sas? and the areas ? which algorithm? where 
is the code?


Is there any program with which one could calculate the volume enclosed by SAS 
resulted from g_sas?


I see different posts in the mailing list addressing the accuracy of g_sas! 
Well, I'm using gmx 3.3.1; is the accompanying g_sas reliable?


Any comment is truthfully appreciated :)

Peyman


P.S. Edmund Husserl believed, that we would indeed be in a nasty position, if 
empirical science were the only kind of science possible. 



--
David van der Spoel, Ph.D., Professor of Biology
Molec. Biophys. group, Dept. of Cell  Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205. Fax: +4618511755.
[EMAIL PROTECTED]   [EMAIL PROTECTED]   http://folding.bmc.uu.se
___
gmx-users mailing listgmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to [EMAIL PROTECTED]

Can't post? Read http://www.gromacs.org/mailing_lists/users.php

Re: [gmx-users] g_sas Vdwradii.dat

2008-06-10 Thread David van der Spoel


maite lopez cabezas wrote:

Hi:
Thanks for the quickly answer. The problem is like David said. g_sas 
use  the Van der Waals radius of the vdwradii.dat file. I want to use 
the same valors that appear in this file but i want to know where they 
were taken for adding the P valor.

Thanks,

Maité


Search the literature for papers about this. I forgot where the current 
values come from, it could well be that they the Eisenhaber paper.


--
David van der Spoel, Ph.D., Professor of Biology
Molec. Biophys. group, Dept. of Cell  Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205. Fax: +4618511755.
[EMAIL PROTECTED]   [EMAIL PROTECTED]   http://folding.bmc.uu.se
___
gmx-users mailing listgmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to [EMAIL PROTECTED]

Can't post? Read http://www.gromacs.org/mailing_lists/users.php

[gmx-users] g_sas Vdwradii.dat

2008-06-07 Thread maite lopez cabezas

Hi:
I'm using g_sas *to analyse a DPPC simulation but it gave the next warning:
WARNING: could not find a Van der Waals radius for 128 atoms
3840 out of 6400 atoms were classified as hydrophobic

I saw that the **Van der Waals radius for phophorous atoms doesn't
appear in vdwraddi.dat. When I modified it and add the **Van der Waals
radius* for this atom and then it works well. But, where were taken
the *Van der Waals radius* for Gromacs? Somebody knows the phophorous
radius for gromacs?
In the literature appears some valors and there aren't the same for
this programs, such as:

Gromacs Other
N 0.1100.155
O 0.1050.152

Thank you in advance,
Maité
___
gmx-users mailing listgmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php

Re: [gmx-users] g_sas Vdwradii.dat

2008-06-07 Thread Xavier Periole


On Sat, 7 Jun 2008 15:04:34 -0400
 maite lopez cabezas [EMAIL PROTECTED] wrote:

Hi:
I'm using g_sas *to analyse a DPPC simulation but it gave the next warning:
WARNING: could not find a Van der Waals radius for 128 atoms
3840 out of 6400 atoms were classified as hydrophobic

I saw that the **Van der Waals radius for phophorous atoms doesn't
appear in vdwraddi.dat. When I modified it and add the **Van der Waals
radius* for this atom and then it works well. But, where were taken
the *Van der Waals radius* for Gromacs? Somebody knows the phophorous
radius for gromacs?

If I am not mistaken the radius used by g_sas are actually defined within
the code and it does not use the ones given in cdwradii.dat.

have a look a the code you'll find them easily.

In the literature appears some valors and there aren't the same for
this programs, such as:

Gromacs Other
N 0.1100.155
O 0.1050.152

Thank you in advance,
Maité


-
XAvier Periole - PhD

NMR  Molecular Dynamics Group
University of Groningen
The Netherlands
-
___
gmx-users mailing listgmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php

Re: [gmx-users] g_sas Vdwradii.dat

2008-06-07 Thread Xavier Periole


On Sat, 07 Jun 2008 22:32:29 +0200
 Xavier Periole [EMAIL PROTECTED] wrote:

On Sat, 7 Jun 2008 15:04:34 -0400
 maite lopez cabezas [EMAIL PROTECTED] wrote:

Hi:
I'm using g_sas *to analyse a DPPC simulation but it gave the next warning:
WARNING: could not find a Van der Waals radius for 128 atoms
3840 out of 6400 atoms were classified as hydrophobic

I saw that the **Van der Waals radius for phophorous atoms doesn't
appear in vdwraddi.dat. When I modified it and add the **Van der Waals
radius* for this atom and then it works well. But, where were taken
the *Van der Waals radius* for Gromacs? Somebody knows the phophorous
radius for gromacs?

If I am not mistaken the radius used by g_sas are actually defined within
the code and it does not use the ones given in cdwradii.dat.

have a look a the code you'll find them easily.

I just had a look at the code. What I said is valid for the gmx-3.1.4.
In gmx-3.3.3 you have:
  /* Get a Van der Waals radius for each atom */
  ndefault = 0;
  for(i=0; (inatoms); i++) {
if (!query_atomprop(atomprop,epropVDW,
*(top-atoms.resname[top-atoms.atom[i].resnr]),
*(top-atoms.atomname[i]),radius[i]))
  ndefault++;
/* radius[i] = calc_radius(*(top-atoms.atomname[i])); */
radius[i] += solsize;
  }

where you can see that the line I was referring to is commented and the
lines above it have been introduced to get the radius from the topology
(I think).
Check the version you use ...

In the literature appears some valors and there aren't the same for
this programs, such as:

Gromacs Other
N 0.1100.155
O 0.1050.152

Thank you in advance,
Maité


-
XAvier Periole - PhD

NMR  Molecular Dynamics Group
University of Groningen
The Netherlands
-
___
gmx-users mailing listgmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the www interface 
or send it to [EMAIL PROTECTED]

Can't post? Read http://www.gromacs.org/mailing_lists/users.php


-
XAvier Periole - PhD

NMR  Molecular Dynamics Group
University of Groningen
The Netherlands
http://md.chem.rug.nl/~periole
-
___
gmx-users mailing listgmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php

Re: [gmx-users] g_sas Vdwradii.dat

2008-06-07 Thread David van der Spoel


Xavier Periole wrote:

On Sat, 07 Jun 2008 22:32:29 +0200
 Xavier Periole [EMAIL PROTECTED] wrote:

On Sat, 7 Jun 2008 15:04:34 -0400
 maite lopez cabezas [EMAIL PROTECTED] wrote:

Hi:
I'm using g_sas *to analyse a DPPC simulation but it gave the next 
warning:

WARNING: could not find a Van der Waals radius for 128 atoms
3840 out of 6400 atoms were classified as hydrophobic

I saw that the **Van der Waals radius for phophorous atoms doesn't
appear in vdwraddi.dat. When I modified it and add the **Van der Waals
radius* for this atom and then it works well. But, where were taken
the *Van der Waals radius* for Gromacs? Somebody knows the phophorous
radius for gromacs?

If I am not mistaken the radius used by g_sas are actually defined within
the code and it does not use the ones given in cdwradii.dat.

have a look a the code you'll find them easily.

I just had a look at the code. What I said is valid for the gmx-3.1.4.
In gmx-3.3.3 you have:
  /* Get a Van der Waals radius for each atom */
  ndefault = 0;
  for(i=0; (inatoms); i++) {
if (!query_atomprop(atomprop,epropVDW,
*(top-atoms.resname[top-atoms.atom[i].resnr]),
*(top-atoms.atomname[i]),radius[i]))
  ndefault++;
/* radius[i] = calc_radius(*(top-atoms.atomname[i])); */
radius[i] += solsize;
  }

where you can see that the line I was referring to is commented and the
lines above it have been introduced to get the radius from the topology
(I think).


No, this does mean that it comes from vdwradii.dat. If there are missing 
atoms you can just add them to the file. The only issue is that there 
are different sets of radii in use. Which one to use depends on the 
application.



--
David van der Spoel, Ph.D., Professor of Biology
Molec. Biophys. group, Dept. of Cell  Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205. Fax: +4618511755.
[EMAIL PROTECTED]   [EMAIL PROTECTED]   http://folding.bmc.uu.se
___
gmx-users mailing listgmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to [EMAIL PROTECTED]

Can't post? Read http://www.gromacs.org/mailing_lists/users.php

[gmx-users] g_sas and vdwradii.dat

2008-06-04 Thread Paul Whitford

Gromacs users,

I have 3 easy questions regarding the use of g_sas

1)  I am trying to understand exactly how gromacs computed the SAS.  I
looked at vdwradii.dat and it says

; Very approximate VanderWaals radii
; only used for drawing atoms as balls or for calculating atomic overlap.

Does atomic overlap include SAS calculations?  If not, where does g_sas get
the sphere sizes when making the calculation?

2) How can I tell gromacs to look at a different file for atom sizes?  I
would like to compare the SAS for a C-alpha model with varying sizes for the
CA beads.

3) How goes g_sas determine which atoms are hydrophobic and hydrophilic?  I
would like to call some CA atoms hydrophobic and others hydrophilic.

Thanks in advance!

-Paul
___
gmx-users mailing listgmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php

[gmx-users] g_sas and PBC

2008-05-25 Thread Gurpreet Singh



Gurpreet Singh wrote:
 Dear Gromacs Users,
 
 I am using g_sas program of gromacs to calculate SASA, ?using
-pbc flag.
 It seems to me that the program does not take into account the
periodic
 boundary conditions.
 Even thought this problem is mentioned in the mailing list, it
still not
 clear whether the program can or cannot take into account the
 periodicity. 
 i am using gromacs3.3.2 . Could anyone please clarify this. 
 


http://bugzilla.gromacs.org/show_bug.cgi?id=180

I downloaded the gromacs 3.3.3 and carried out some test
calculations. The PBC is still not working, at least with test i
have performed.
I generated a trajcetory file containing two atoms in a cubic
box of 4nm having same x and y coordinates and varied the z
coordinates of one of the atoms.
one atom is fixed at z coordinate of 3.9. The result of sasa vs
coordinates is as follows:
   
Step noz coordinate total_sasa
   1 2.0500074506   14.1497
   2 2.1000149012   14.1497
   3 2.1500223517   14.1497
   4 2.2000298023   14.1497
   5 2.2500372529   14.1497
   6 2.3000447035   14.1497
   7 2.3500521541   14.1497
   8 2.4000596046   14.1497
   9 2.4500670552   14.1497
  10 2.5000745058   14.1497
  11 2.5500819564   14.1497
  12 2.6000894070   14.1497
  13 2.6500968575   14.1497
  14 2.7001043081   14.1497
  15 2.7501117587   14.1497
  16 2.8001192093   14.1497
  17 2.8501266599   14.1497
  18 2.9001341105   14.1497
  19 2.9501415610   14.1497
  20 3.0001490116   14.1497
  21 3.0501564622   14.1497
  22 3.1001639128   14.1497
  23 3.1501713634   14.1497
  24 3.2001788139   14.1497
  25 3.2501862645   14.1497
  26 3.3001937151   14.1497
  27 3.3502011657   13.7971
  28 3.4002086163   13.1359
  29 3.4502160668   12.5849
  30 3.5002235174   11.9237
  31 3.5502309680   11.3727
  32 3.6002384186   10.7115
  33 3.6502458692   10.1605
  34 3.7002533197   9.49926
  35 3.7502607703   8.94826
  36 3.8002682209   8.39726
  37 3.8502756715   7.51566
  38 3.9002831221   14.1497
  39 3.9502905726   7.51566
  402.980232238769531E-008  14.1497
  415.03054738045E-002  14.1497
  420.10031292439   14.1497
  430.15032037497   14.1497
  440.20032782555   14.1497
  450.25033527613   14.1497
  460.30034272671   14.1497
  470.35035017729   14.1497
  480.40035762787   14.1497
  490.45036507845   14.1497
  500.50037252903   14.1497
  510.55037997961   14.1497
  520.60038743019   14.1497
  530.65039488077   14.1497
  540.70040233135   14.1497
  550.75040978193   14.1497



I used the following command to calculate the sasa
g_sas_d -f test.xtc -s topol.tpr -pbc -ndots 500 

I can attached the tpr and xtc file if needed

With Regards,
Gurpreet singh

___
gmx-users mailing listgmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php

Re: [gmx-users] g_sas and PBC

2008-05-25 Thread David van der Spoel


Gurpreet Singh wrote:

  

Gurpreet Singh wrote:
  Dear Gromacs Users,
 
  I am using g_sas program of gromacs to calculate SASA, ?using
-pbc flag.
  It seems to me that the program does not take into account the
periodic
  boundary conditions.
  Even thought this problem is mentioned in the mailing list, it
still not
  clear whether the program can or cannot take into account the
  periodicity.
  i am using gromacs3.3.2 . Could anyone please clarify this.
 


http://bugzilla.gromacs.org/show_bug.cgi?id=180

I downloaded the gromacs 3.3.3 and carried out some test
calculations. The PBC is still not working, at least with test i
have performed.
I generated a trajcetory file containing two atoms in a cubic box of
4nm having same x and y coordinates and varied the z coordinates of
one of the atoms.
one atom is fixed at z coordinate of 3.9. The result of sasa vs
coordinates is as follows:
  
Step noz coordinate total_sasa

   1 2.0500074506   14.1497
   2 2.1000149012   14.1497
   3 2.1500223517   14.1497
   4 2.2000298023   14.1497
   5 2.2500372529   14.1497
   6 2.3000447035   14.1497
   7 2.3500521541   14.1497
   8 2.4000596046   14.1497
   9 2.4500670552   14.1497
  10 2.5000745058   14.1497
  11 2.5500819564   14.1497
  12 2.6000894070   14.1497
  13 2.6500968575   14.1497
  14 2.7001043081   14.1497
  15 2.7501117587   14.1497
  16 2.8001192093   14.1497
  17 2.8501266599   14.1497
  18 2.9001341105   14.1497
  19 2.9501415610   14.1497
  20 3.0001490116   14.1497
  21 3.0501564622   14.1497
  22 3.1001639128   14.1497
  23 3.1501713634   14.1497
  24 3.2001788139   14.1497
  25 3.2501862645   14.1497
  26 3.3001937151   14.1497
  27 3.3502011657   13.7971
  28 3.4002086163   13.1359
  29 3.4502160668   12.5849
  30 3.5002235174   11.9237
  31 3.5502309680   11.3727
  32 3.6002384186   10.7115
  33 3.6502458692   10.1605
  34 3.7002533197   9.49926
  35 3.7502607703   8.94826
  36 3.8002682209   8.39726
  37 3.8502756715   7.51566
  38 3.9002831221   14.1497
  39 3.9502905726   7.51566
  402.980232238769531E-008  14.1497
  415.03054738045E-002  14.1497
  420.10031292439   14.1497
  430.15032037497   14.1497
  440.20032782555   14.1497
  450.25033527613   14.1497
  460.30034272671   14.1497
  470.35035017729   14.1497
  480.40035762787   14.1497
  490.45036507845   14.1497
  500.50037252903   14.1497
  510.55037997961   14.1497
  520.60038743019   14.1497
  530.65039488077   14.1497
  540.70040233135   14.1497
  550.75040978193   14.1497


I used the following command to calculate the sasa
g_sas_d -f test.xtc -s topol.tpr -pbc -ndots 500

I can attached the tpr and xtc file if needed



Please reopen the bugzilla and send your input there.



With Regards,
Gurpreet singh




___
gmx-users mailing listgmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to [EMAIL PROTECTED]

Can't post? Read http://www.gromacs.org/mailing_lists/users.php



--
David van der Spoel, Ph.D.
Molec. Biophys. group, Dept. of Cell  Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205. Fax: +4618511755.
[EMAIL PROTECTED]   [EMAIL PROTECTED]   http://folding.bmc.uu.se
___
gmx-users mailing listgmx-users@gromacs.org

[gmx-users] g_sas and PBC

2008-05-24 Thread Gurpreet Singh

Dear Gromacs Users,

I am using g_sas program of gromacs to calculate SASA, using -pbc flag.
It seems to me that the program does not take into account the periodic
boundary conditions.
Even thought this problem is mentioned in the mailing list, it still not
clear whether the program can or cannot take into account the
periodicity. 
i am using gromacs3.3.2 . Could anyone please clarify this. 

With Regards,
Gurpreet Singh











































___
gmx-users mailing listgmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php

Re: [gmx-users] g_sas and PBC

2008-05-24 Thread David van der Spoel


Gurpreet Singh wrote:

Dear Gromacs Users,

I am using g_sas program of gromacs to calculate SASA, ?using -pbc flag.
It seems to me that the program does not take into account the periodic
boundary conditions.
Even thought this problem is mentioned in the mailing list, it still not
clear whether the program can or cannot take into account the
periodicity. 
i am using gromacs3.3.2 . Could anyone please clarify this. 




http://bugzilla.gromacs.org/show_bug.cgi?id=180


With Regards,
Gurpreet Singh















































___
gmx-users mailing listgmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to [EMAIL PROTECTED]

Can't post? Read http://www.gromacs.org/mailing_lists/users.php



--
David.

David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  75124 Uppsala, Sweden
phone:  46 18 471 4205  fax: 46 18 511 755
[EMAIL PROTECTED]   [EMAIL PROTECTED]   http://folding.bmc.uu.se

___
gmx-users mailing listgmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to [EMAIL PROTECTED]

Can't post? Read http://www.gromacs.org/mailing_lists/users.php

[gmx-users] g_sas and vdwradii.dat

2008-03-31 Thread Justin A. Lemkul


Hi all,

I recently completed several simulations of pure DPPC bilayers (128 lipids, 64
per leaflet, from Tieleman's site), and am processing the output.  Of interest
to me is the SASA, so I'm using g_sas.  I ran the command:

g_sas -f md_0_100.xtc -s md.tpr -n sas.ndx

(selecting solvent for the calculation, and a subset of my lipids for output)

I get the following message:

0 out of 3200 atoms were classified as hydrophobic

But yet, if I let the calculation go anyway, I get seemingly reasonable values
for hydrophobic, hydrophilic, and total SASA.  It is odd to me that in a
membrane, none of the atoms are considered hydrophobic.

Should I be concerned about my results being incorrect, or is it simply because
the atom types of the acyl chains are unrecognized as standard by g_sas?  I
have learned not to ignore such strange messages :-)

Thanks in advance.

-Justin



Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
[EMAIL PROTECTED] | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/


___
gmx-users mailing listgmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php

Re: [gmx-users] g_sas WARNING: could not find a Van der Waals radius

2008-03-30 Thread Tsjerk Wassenaar

Hi Jo,

   Also if I am comparing the SASA for the enzyme in
   three different simulations were only the ligand (for which all radii are
   defined) differs, would this have a huge effect on the results?

Your question is semantically garbled. You comparing anything should
not influence the results (otherwise you're doing something terribly
wrong). If the question is whether the ligand has a (huge) effect on
the SASA, that's what the comparison is for. The meta-question whether
the (putative) influence on the SASA is due to an effect of the ligand
on the protein or an effect of the ligand in the SASA measurement
itself, can not be answered from here. It's for you to analyze.

Cheers,

Tsjerk

-- 
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623
___
gmx-users mailing listgmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php

1 2 >

1 - 100 of 126 matches

Mail list logo