[gmx-users] g_sas

Hello, I am interested in using g_sas in gromacs 4.6.5. I have a few questions: 1.) Is it advisable to use this tool to compute the vacuum accessible surface area for a liquid? 2.) I ran a test using .gro / .trr / .tpr output from a production run in my workflow as shown follows: { g_sas -f A.gr

[gmx-users] g_sas

Dear Gromacs users, I want to calculate the hydrophobic and hydrophilic area of a protein by using the g_sas command. I have used: g_sas -f md.xtc -s md.tpr -o area.xvg -tv volume.xvg However, looking at the area.xvg with xmgrace, I can only see the hydrophobic area not the hydrophilic.

Re: [gmx-users] g_sas

Hi Eric, 1) Yes. Use a probe radius of 0 nm. 2) No. There is no verbose option in g_sas AFAIK. As an aside, you may want to reconsider -xvg none 3) No difference in my experience. 4) g_sas uses vdwradii.dat, which may not have the vdw radius for a particular atom type. Eg: Phosphorus is not present

Re: [gmx-users] g_sas

Hi Eric, Sorry, I misread your mail. You cannot compute the vacuum accessible surface area for a liquid because the molecules are in constant motion. Regards, On Sat, Aug 16, 2014 at 9:15 PM, rajat desikan wrote: > Hi Eric, > 1) Yes. Use a probe radius of 0 nm. > 2) No. There is no verbose opt

Re: [gmx-users] g_sas

ajat desikan > To: Discussion list for GROMACS users > Subject: Re: [gmx-users] g_sas > Message-ID: > < > ca+d_lwtqq+0gphtq+8wqholrfqbwy6ycz6q-i4yag7hwmzh...@mail.gmail.com> > Content-Type: text/plain; charset=UTF-8 > > Hi Eric, > Sorry, I misread your ma

Re: [gmx-users] g_sas

Whether or not that output is meaningful to you is up to you; I have never dealt in vacuum-accessible SA. -Justin Thanks again Rajat, Best, Eric Message: 7 Date: Sat, 16 Aug 2014 21:17:36 +0530 From: rajat desikan To: Discussion list for GROMACS users Subject: Re: [gmx-users] g_sas Message-ID

Re: [gmx-users] g_sas

> This should not be necessary; you can provide the trajectory and g_sas > should do this for you. Whether or not that output is meaningful to you is > up to you; I have never dealt in vacuum-accessible SA. > > -Justin > > Thanks again Rajat, >> >> Best, >>

Re: [gmx-users] g_sas

king for some way to obtain a time-averaged atom-composition > >> of > >> the liquid surface. If g_sas can be used for temporal snaphot .gro file, > >> perhaps I can extract a variety of timesteps and carry out the > calculation > >> manually. >

Re: [gmx-users] g_sas

On 8/16/14, 9:09 PM, Eric Smoll wrote: Hello Rajat and Justin, I am deeply grateful for the responses. Thank you. Rajat, You said: "By vacuum accessible surface area, I assume that you mean the area defined the surface of the interstitial volume." I am looking for the vacuum accessible surf

Re: [gmx-users] g_sas

gt;> > > >> Surely we can define a vacuum accessible surface for any timestep of > > this > > >> trajectory, correct? I agree that molecules at the surface are > > constantly > > >> changing making the definition of a surface ill-defined over a >

[gmx-users] g_sas area

Dear all, I just wanna calculate the SAS of a protein in a protein-in-water binary system, when I use g_sas, it asks me for a caculation group and output group, I wonder how I should make the selection in this case. And what would be the meaning if I choose the whole system for both groups? T

[gmx-users] g_sas dG

Dear all, I just wanna calculate the SAS of a protein (ubiquitin) in a protein-in-water binary system, when I use g_sas, it asks me for a caculation group and output group, I chose the whole protein as both groups. However, the solvation free energy (dG) is positive and a bit large, ~ +300 KJ/

[gmx-users] g_sas problem?

Hello: I am interested in the solvent access surface area change after ligand binding to protein. I performed protein/ligand complex MD in Gromacs. I try to obtain SASA with command: g_sas_mpi -f nvt.xtc -nopbc -s nvt-4.tpr -o area.xvg -n Reading frame 0 time0.000 Select a group

[gmx-users] g_sas question

Hello, I am using the Gromacs 4.6.5 g_sas tool with custom radii for each atom as specified with a local vdwradii.dat file. Are the surface areas reported in "-or atomarea.xvg" on a sphere defined by R_VDW or at R_VDW + R_probe? Similarly, is the "-minarea #" flag a threshold value that applies

Re: [gmx-users] g_sas

Dear Cristina, how did you call xmgrace? Did you supply the "-nxy" switch before area.xvg or volume.xvg? Regards, Andras On 05/28/2018 09:45 AM, Gonzalez Fernandez, Cristina wrote: > Dear Gromacs users, > > > > > > I want to calculate the hydrophobic and hydrophilic area of a protein by > usi

Re: [gmx-users] g_sas area

Hello Yao, Running "g_sas -h" will print out some helpful information. It reads: "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." Best, Eric On Mon, Aug 18, 2014 at 10:00 AM, xy21hb w

Re: [gmx-users] g_sas dG

On 2014-08-19 11:30, xy21hb wrote: Dear all, I just wanna calculate the SAS of a protein (ubiquitin) in a protein-in-water binary system, when I use g_sas, it asks me for a caculation group and output group, I chose the whole protein as both groups. However, the solvation free energy (dG) is

Re: [gmx-users] g_sas problem?

On 1/5/15 4:01 PM, Albert wrote: Hello: I am interested in the solvent access surface area change after ligand binding to protein. I performed protein/ligand complex MD in Gromacs. I try to obtain SASA with command: g_sas_mpi -f nvt.xtc -nopbc -s nvt-4.tpr -o area.xvg -n Reading frame

Re: [gmx-users] g_sas problem?

Thanks a lot for the reply. I believe this 122 atoms belong to my ligand. I generate the ligand.itp file by acpype tool and the system was assigned for Amber FF. BTW, why does g_sas ask twice to select a group for output as following? and a group for output: Select a group: 26 Selected 26: 'P

Re: [gmx-users] g_sas problem?

On 1/6/15 2:33 AM, Albert wrote: Thanks a lot for the reply. I believe this 122 atoms belong to my ligand. I generate the ligand.itp file by acpype tool and the system was assigned for Amber FF. BTW, why does g_sas ask twice to select a group for output as following? Read the help descript

Re: [gmx-users] g_sas problem?

I've already read g_sasa -h and related section in Gromacs manual. But I didn't find anything useful. There are mainly about each option.. Could you please give some comments? THX On 01/06/2015 11:29 AM, Justin Lemkul wrote: Read the help description. -Justin -- Gromacs Users mail

Re: [gmx-users] g_sas problem?

On 1/6/15 5:41 AM, Albert wrote: I've already read g_sasa -h and related section in Gromacs manual. But I didn't find anything useful. There are mainly about each option.. Could you please give some comments? This is why you need two selections: "The program requires a selection for

[gmx-users] g_sas - General Information

Hello, I am trying to use the g_sas tool in order to conduct some analysis. This is a simple question but I was unable to find an adequate answer in the archives. What are the quantities that are output by g_sas when -tv is called and their physical meaning? What do the units nm\S3\N mean? Also

Re: [gmx-users] g_sas - General Information

, 2015 11:22 AM To: gromacs.org_gmx-users@maillist.sys.kth.se Subject: [gmx-users] g_sas - General Information Hello, I am trying to use the g_sas tool in order to conduct some analysis. This is a simple question but I was unable to find an adequate answer in the archives. What are the quantities

[gmx-users] g_sas values of zero and Warning

HI All, I'm trying to get a measure of the solvent accessible surface area of a protein's catalytic site. It is unknown precisely how the substrate actually fits in the site given that in the crystal structure the site it too enclosed for the bulky substrate. I am using a progressive measure of

[gmx-users] g_sas: unable to reproduce data from original article of the DCLM (Eisenhaber1995)

Dear all, I have been having some puzzling results when using g_sas to analyze some trajectories, so I have decided to go back to basics. As described in the documentation, g_sas implements the double cubic lattice method (DCLM) originally presented in Eisenhaber1995 (doi: 10.1002/jcc.540160303 <

Re: [gmx-users] g_sas: unable to reproduce data from original article of the DCLM (Eisenhaber1995)

On 2014-02-22 18:34, João M. Damas wrote: Dear all, I have been having some puzzling results when using g_sas to analyze some trajectories, so I have decided to go back to basics. As described in the documentation, g_sas implements the double cubic lattice method (DCLM) originally presented in

Re: [gmx-users] g_sas: unable to reproduce data from original article of the DCLM (Eisenhaber1995)

Hello David, Thank you for your fast reply and your suggestions! The results are in Attached Table 2 (see below). - I followed your PBC suggestion, but used the -pbc flag instead (I still ended up doing yours, read further ahead). While turning off PBC for GMX4.0.4 leaves the results unc

Re: [gmx-users] g_sas: unable to reproduce data from original article of the DCLM (Eisenhaber1995)

Hi, Thanks for the report. In relation to https://gerrit.gromacs.org/#/c/2726/I had been planning to add some tests for the actual algorithm used, and this report made me prioritize this. Here's an intermediate result. I have not yet tested the PBC-enabled computation at all, and haven't looked at

Re: [gmx-users] g_sas: unable to reproduce data from original article of the DCLM (Eisenhaber1995)

Hi, On Thu, Feb 27, 2014 at 4:09 PM, Teemu Murtola wrote: > I'll post additional information once I have had time to test more cases. > I have now created to track the issue, and uploaded a fix to Gerrit: . My current

Re: [gmx-users] g_sas: unable to reproduce data from original article of the DCLM (Eisenhaber1995)

Hello Teemu, Thank you! I am glad the GROMACS team is concerned about this particular problem. And I am sorry for my late reply. For the sake of conciseness, so we do not get lost in the data, I am only showing the single precision results (we may bring double precision later on again). Also, sin

Re: [gmx-users] g_sas: unable to reproduce data from original article of the DCLM (Eisenhaber1995)

On 2014-03-04 04:39, João M. Damas wrote: Hello Teemu, Thank you! I am glad the GROMACS team is concerned about this particular problem. And I am sorry for my late reply. For the sake of conciseness, so we do not get lost in the data, I am only showing the single precision results (we may bring

Re: [gmx-users] g_sas: unable to reproduce data from original article of the DCLM (Eisenhaber1995)

Done: http://redmine.gromacs.org/issues/1449 João On Tue, Mar 4, 2014 at 6:56 AM, David van der Spoel wrote: > On 2014-03-04 04:39, João M. Damas wrote: > >> Hello Teemu, >> >> Thank you! I am glad the GROMACS team is concerned about this particular >> problem. >> And I am sorry for my late rep

Re: [gmx-users] g_sas: unable to reproduce data from original article of the DCLM (Eisenhaber1995)

Thanks to Teemu, we found that the "-pbc yes" results is not a bug after all (my bad). It is solved here: http://redmine.gromacs.org/issues/1449. The final results are in Attached Table 4. To conclude, going back to the "-nopbc" bug found, the following plot is a "real case" example of the differe

Re: [gmx-users] g_sas: unable to reproduce data from original article of the DCLM (Eisenhaber1995)

Sorry, I shouldn't have embedded the plot. Here goes a link to it: https://dl.dropboxusercontent.com/u/384/plot_fixed_vs_nonfixed_g_sas.png On Wed, Mar 5, 2014 at 2:27 AM, João M. Damas wrote: > Thanks to Teemu, we found that the "-pbc yes" results is not a bug after > all (my bad). It is

Re: [gmx-users] g_sas: unable to reproduce data from original article of the DCLM (Eisenhaber1995)

Thanks, Joao! (And David and Teemu!) Mark On Mar 5, 2014 11:11 AM, "João M. Damas" wrote: > Sorry, I shouldn't have embedded the plot. Here goes a link to it: > > > https://dl.dropboxusercontent.com/u/384/plot_fixed_vs_nonfixed_g_sas.png > > > On Wed, Mar 5, 2014 at 2:27 AM, João M. Damas w