[gmx-users] g_sas
João M. Damas
jmdamas at itqb.unl.pt
Sun Aug 17 18:41:31 CEST 2014
How are you making the export GMXLIB? Check that or try putting a copy
of vdwradii.dat
on ./ instead.
Use -debug 1 as Justin suggested and check the debug output for the radius
that are being used by g_sas.
João
On Sun, Aug 17, 2014 at 2:09 AM, Eric Smoll <ericsmoll at gmail.com> 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 surface area at a vacuum-liquid
> interface. I am very sorry for the confusion. Instead of carrying on with a
> conversation on the nature of the g_sas simulation output, perhaps I should
> just try to get a surface calculation working and examine it myself.
>
> Rajat and Justin,
>
> The file "vdwradii.dat" only appears in a few places in the manual and it
> is unclear if g_sas actually uses it. I made a local copy of
> share/gromacs/top, edited vdwradii.dat with the following format
> {3-LETTER-RESIDUE-NAME .TOP/.GRO-FILE-ATOM-NAME RADIUS-IN-NM} and
> updated the GMXLIB environment variable to point to this edited directory
> with "export path/to/new/top". I created a .tpr file with grompp and made a
> call with g_sas as I described before. I get the same error:
>
> WARNING: Masses and atomic (Van der Waals) radii will be guessed
> based on residue and atom names, since they could not be
> definitively assigned from the information in your input
> files. These guessed numbers might deviate from the mass
> and radius of the atom type. Please check the output
> files if necessary.
>
> WARNING: could not find a Van der Waals radius for 640 atoms
> 29440 out of 34560 atoms were classified as hydrophobic
>
> As I mentioned before, 640 matches the number of molecules I have in the
> simulation. I have no idea why the g_sas is not referencing the sigma
> values in my ffnonbonded file or my vdwradii.dat. I have used vim regular
> expression capabilities to ensure that every atom in my .gro/.top files is
> represented in the vdwradii.dat file. More guidance would be much
> appreciated.
>
> Thanks again for your help Justin and Rajat,
>
> Best,
> Eric
>
>
>
>
>
>
>
> On Sat, Aug 16, 2014 at 12:53 PM, rajat desikan <rajatdesikan at gmail.com>
> wrote:
>
> > Hi Eric,
> > By vacuum accessible surface area, I assume that you mean the area
> defined
> > the surface of the interstitial volume. In my understanding, using g_sas
> > will give you the solvent accessible area (non buried area) averaged over
> > all the molecules and the trajectory. This is different from the
> > interstitial surface area. Someone please correct me if I am wrong.
> >
> > Justin is correct when he says that the program displays time frames as
> it
> > analyses the trajectory. From your description, I feel that g_sas is
> stuck
> > on the first frame itself since it is calculating over all the liquid
> > molecules. And there is no way to figure out how much of that frame has
> > been analysed. What is your system made of?
> >
> > I am not sure what you mean when you say trajectory like information.
> g_sas
> > prints out information for every time step.
> >
> > Regards,
> >
> > On Saturday, August 16, 2014, Justin Lemkul <jalemkul at vt.edu> wrote:
> >
> > >
> > >
> > > On 8/16/14, 1:40 PM, Eric Smoll wrote:
> > >
> > >> Rajat,
> > >>
> > >> Thank you for the rapid response. It is very helpful.
> > >>
> > >> "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
> > >>
> > >
> > > #2 is incorrect; all Gromacs programs print out which frame they are
> > > working on to the terminal.
> > >
> > > 3) No difference in my experience."
> > >>
> > >> Let me get this straight. You are saying that analyzing a .trr outputs
> > an
> > >> average, not trajectory-like information. You are saying, for your
> > >> specific
> > >> system, you see little difference in the surface formed from
> analyzing a
> > >> trajectory and analyzing a snapshot. That may be for a protein but I
> am
> > >> studying a molecular liquid.
> > >>
> > >>
> > > The type of output depends on what you ask for in your command line.
> The
> > > use of -o will give you a time series of all the frames in your
> > trajectory.
> > >
> > > "4) g_sas uses vdwradii.dat, which may not have the vdw radius for a
> > >> particular atom type. Eg: Phosphorus is not present by default in
> > >> vdwradii.dat (for phosphorylated proteins). You may add this manually
> > to a
> > >> local copy of vdwradii.dat"
> > >>
> > >> Thank you. Exactly, the information I was looking for!
> > >>
> > >> "Sorry, I misread your mail. You cannot compute the vacuum accessible
> > >> surface area for a liquid because the molecules are in constant
> motion."
> > >>
> > >> So are you saying that *I cannot use g_sas to compute the vacuum
> > >> accessible
> > >> surface area for a liquid at all* or *I cannot use g_sas to compute
> the
> > >> vacuum accessible surface area with a trajectory*?
> > >>
> > >> 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
> > trajectory
> > >> but I am looking 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.
> > >>
> > >>
> > > 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,
> > >> Eric
> > >>
> > >>
> > >> Message: 7
> > >>> Date: Sat, 16 Aug 2014 21:17:36 +0530
> > >>> From: rajat desikan <rajatdesikan at gmail.com>
> > >>> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> > >>> Subject: Re: [gmx-users] g_sas
> > >>> Message-ID:
> > >>> <
> > >>> CA+d_LwtqQ+0GPhTQ+8WQhoLrfQbwY6Ycz6Q-i4YAg7HwmzHe-A at mail.gmail.com>
> > >>> Content-Type: text/plain; charset=UTF-8
> > >>>
> > >>> 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 <
> rajatdesikan at gmail.com
> > >
> > >>> wrote:
> > >>>
> > >>> 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 by default in
> > >>>> vdwradii.dat (for phosphorylated proteins). You may add this
> manually
> > to
> > >>>>
> > >>> a
> > >>>
> > >>>> local copy of vdwradii.dat
> > >>>>
> > >>>> Regards,
> > >>>>
> > >>>>
> > >>>> On Sat, Aug 16, 2014 at 9:01 PM, Eric Smoll <ericsmoll at gmail.com>
> > >>>> wrote:
> > >>>>
> > >>>> 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.gro -s A.tpr -o TEST1.xvg
> > >>>>>
> > >>>> -xvg
> > >>>
> > >>>> none -b 2000 -e 4000 -probe 0.15 -pbc -minarea 0.2 -ndots 24 -i
> > >>>>>
> > >>>> TEST1.itp;
> > >>>
> > >>>> g_sas -f A.trr -s A.tpr -o TEST2.xvg -xvg none -b 2000 -e 4000
> -probe
> > >>>>>
> > >>>> 0.15
> > >>>
> > >>>> -pbc -minarea 0.2 -ndots 24 -i TEST2.itp }. The .trr / .tpr run
> > produces
> > >>>>> no
> > >>>>> output while processing so it is unclear when it will end. Is there
> > >>>>>
> > >>>> anyway
> > >>>
> > >>>> to enable output that will report on the progress of the
> calculation?
> > >>>>>
> > >>>>> 3.) What are the difference in output when processing a .gro vs a
> > .trr?
> > >>>>> Does trajectory input produce trajectory output or some sort of
> > >>>>> average?
> > >>>>>
> > >>>>> 4.) When running on the .gro / .tpr combination I received the
> > >>>>> following
> > >>>>> error:
> > >>>>>
> > >>>>> WARNING: Masses and atomic (Van der Waals) radii will be guessed
> > >>>>> based on residue and atom names, since they could not be
> > >>>>> definitively assigned from the information in your input
> > >>>>> files. These guessed numbers might deviate from the mass
> > >>>>> and radius of the atom type. Please check the output
> > >>>>> files if necessary.
> > >>>>>
> > >>>>> WARNING: could not find a Van der Waals radius for 640 atoms
> > >>>>> 29440 out of 34560 atoms were classified as hydrophobic
> > >>>>>
> > >>>>> Note that I am using 640 molecules in my liquid simulation. I have
> > not
> > >>>>> received this error for any other step in my molecular dynamics
> > >>>>>
> > >>>> workflow.
> > >>>
> > >>>> It concerns me. Is this an indication that my coordinate and
> parameter
> > >>>>> files are somehow incomplete? How do I go about troubleshooting
> this
> > >>>>> and
> > >>>>> specifying the missing parameters?
> > >>>>>
> > >>>>> Best,
> > >>>>> Eric
> > >>>>> --
> > >>>>> Gromacs Users mailing list
> > >>>>>
> > >>>>> * Please search the archive at
> > >>>>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > >>>>> posting!
> > >>>>>
> > >>>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > >>>>>
> > >>>>> * For (un)subscribe requests visit
> > >>>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
> > or
> > >>>>> send a mail to gmx-users-request at gromacs.org.
> > >>>>>
> > >>>>>
> > >>>>
> > >>>>
> > >>>> --
> > >>>> Rajat Desikan (Ph.D Scholar)
> > >>>> Prof. K. Ganapathy Ayappa's Lab (no 13),
> > >>>> Dept. of Chemical Engineering,
> > >>>> Indian Institute of Science, Bangalore
> > >>>>
> > >>>>
> > >>>
> > >>>
> > >>> --
> > >>> Rajat Desikan (Ph.D Scholar)
> > >>> Prof. K. Ganapathy Ayappa's Lab (no 13),
> > >>> Dept. of Chemical Engineering,
> > >>> Indian Institute of Science, Bangalore
> > >>>
> > >>>
> > > --
> > > ==================================================
> > >
> > > Justin A. Lemkul, Ph.D.
> > > Ruth L. Kirschstein NRSA Postdoctoral Fellow
> > >
> > > Department of Pharmaceutical Sciences
> > > School of Pharmacy
> > > Health Sciences Facility II, Room 601
> > > University of Maryland, Baltimore
> > > 20 Penn St.
> > > Baltimore, MD 21201
> > >
> > > jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> > > http://mackerell.umaryland.edu/~jalemkul
> > >
> > > ==================================================
> > > --
> > > Gromacs Users mailing list
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> > >
> >
> >
> > --
> > Rajat Desikan (Ph.D Scholar)
> > Prof. K. Ganapathy Ayappa's Lab (no 13),
> > Dept. of Chemical Engineering,
> > Indian Institute of Science, Bangalore
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
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--
João M. Damas
PhD Student
Protein Modelling Group
ITQB-UNL, Oeiras, Portugal
Tel:+351-214469613
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