[gmx-users] G_rmsf, reference structur

Tue Apr 7 10:25:09 CEST 2015

Hi Tsjerk,

thanks for your fast answer!
But did you got this information from the -help option or from the code?
Because to me the help option of g_rmsf is a bit ambigous.

Floris

On Fri, Apr 3, 2015 at 5:53 PM, <
gromacs.org_gmx-users-request at maillist.sys.kth.se> wrote:

> Send gromacs.org_gmx-users mailing list submissions to
>         gromacs.org_gmx-users at maillist.sys.kth.se
>
> To subscribe or unsubscribe via the World Wide Web, visit
>         https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
> or, via email, send a message with subject or body 'help' to
>         gromacs.org_gmx-users-request at maillist.sys.kth.se
>
> You can reach the person managing the list at
>         gromacs.org_gmx-users-owner at maillist.sys.kth.se
>
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of gromacs.org_gmx-users digest..."
>
>
> Today's Topics:
>
>    1. G_rmsf, reference structure (Eerden, van, F.J.)
>    2. Re: G_rmsf, reference structure (Tsjerk Wassenaar)
>    3. Re: GMX-compatible DNA coordinates (Alex)
>    4. Re: GMX-compatible DNA coordinates (Tsjerk Wassenaar)
>    5. Re: GMX-compatible DNA coordinates (Mark Abraham)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Fri, 3 Apr 2015 12:36:28 +0200
> From: "Eerden, van, F.J." <f.j.van.eerden at rug.nl>
> To: gromacs.org_gmx-users at maillist.sys.kth.se
> Subject: [gmx-users] G_rmsf, reference structure
> Message-ID:
>         <CAFaYwfjrzJ7HCXYLiJQwBQZmCnoAy+69o=
> eOdYU50YsWxeOe+A at mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> Dears,
>
> I have calculated the RMSF from a protein trajectory in Gromacs 4.5.5.
>
> My question is how the RMSF is calculated:
> A)
> 1) fitting of the trajectory to the tpr file supplied by -s
> 2) calculating the averaged atom coordinates over time (x~)
> 3) calculating the deviation from the averaged structure (x-x~), for each
> time frame
> 4) averaging over all time frames <x-x~>
>
> OR
> B)
> 1) fitting of the trajectory to the tpr file supplied by -s
> 2) calculating the deviation from the TPR structure (x-x*), for each time
> frame
> 3) averaging over all time frames <x-x*>
>
> This question has already popped up multiple times in the mailing list:
> https://www.mail-archive.com/gmx-users@gromacs.org/msg25391.html
> and
> http://comments.gmane.org/gmane.science.biology.gromacs.user/38359
>
> The problem is that there are multiple answers given:
> In the first one, it is argued that method A is used
> in the second mailing list, Marc Abraham states that method B is being
> used, while Tsjerk mentions method A.
>
> I tried to resolve this by looking into thee source code,
> and although to me it seems that it is option, B, I do not trust my Gromacs
> code reading capabilities that well ;)
>
> Happy Easter!
>
> Floris
>
>
> ------------------------------
>
> Message: 2
> Date: Fri, 3 Apr 2015 13:13:02 +0200
> From: Tsjerk Wassenaar <tsjerkw at gmail.com>
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Subject: Re: [gmx-users] G_rmsf, reference structure
> Message-ID:
>         <CABzE1SgJdhy_dnK86vU0LeduuGDWMPw4Rx=
> 6R_SNxCGQwsNhLQ at mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> Hi Floris,
>
> By default it's A. There is an option for doing B. But B makes no sense.
>
> Cheers,
>
> Tsjerk
> On Apr 3, 2015 1:10 PM, "Eerden, van, F.J." <f.j.van.eerden at rug.nl> wrote:
>
> > Dears,
> >
> > I have calculated the RMSF from a protein trajectory in Gromacs 4.5.5.
> >
> > My question is how the RMSF is calculated:
> > A)
> > 1) fitting of the trajectory to the tpr file supplied by -s
> > 2) calculating the averaged atom coordinates over time (x~)
> > 3) calculating the deviation from the averaged structure (x-x~), for each
> > time frame
> > 4) averaging over all time frames <x-x~>
> >
> > OR
> > B)
> > 1) fitting of the trajectory to the tpr file supplied by -s
> > 2) calculating the deviation from the TPR structure (x-x*), for each time
> > frame
> > 3) averaging over all time frames <x-x*>
> >
> > This question has already popped up multiple times in the mailing list:
> > https://www.mail-archive.com/gmx-users@gromacs.org/msg25391.html
> > and
> > http://comments.gmane.org/gmane.science.biology.gromacs.user/38359
> >
> > The problem is that there are multiple answers given:
> > In the first one, it is argued that method A is used
> > in the second mailing list, Marc Abraham states that method B is being
> > used, while Tsjerk mentions method A.
> >
> > I tried to resolve this by looking into thee source code,
> > and although to me it seems that it is option, B, I do not trust my
> Gromacs
> > code reading capabilities that well ;)
> >
> > Happy Easter!
> >
> > Floris
> > --
> > 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.
> >
>
>
> ------------------------------
>
> Message: 3
> Date: Fri, 3 Apr 2015 07:40:26 -0600
> From: Alex <nedomacho at gmail.com>
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Subject: Re: [gmx-users] GMX-compatible DNA coordinates
> Message-ID: <1795469025.20150403074026 at gmail.com>
> Content-Type: text/plain; charset="us-ascii"
>
> An HTML attachment was scrubbed...
> URL: <
> http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20150403/47274e09/attachment-0001.html
> >
>
> ------------------------------
>
> Message: 4
> Date: Fri, 3 Apr 2015 16:47:25 +0200
> From: Tsjerk Wassenaar <tsjerkw at gmail.com>
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>,  Alex
>         <nedomacho at gmail.com>
> Subject: Re: [gmx-users] GMX-compatible DNA coordinates
> Message-ID:
>         <CABzE1SgeVaCK+zLje+fWDbR-C+qWnZ47Yc-Ans9jqhc0Tx=
> J1A at mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> Hi Alex,
>
> You've solved the issue of getting a DNA structure, but now you're facing a
> problem of getting Gromacs to prune it. That has to do with the naming
> scheme mainly. Your best bet is using sed to do name substitution. Probably
> google will give some good hints about such substitutions in PDB files.
>
> Cheers,
>
> Tsjerk
> On Apr 3, 2015 3:40 PM, "Alex" <nedomacho at gmail.com> wrote:
>
> >  Mark,
> >
> >
> > Not to troll, but why did you assume that I didn't do my due diligence
> > before posting here?
> >
> > Because, you see, you could have left that second part of your reply
> > (which only confirms the legitimacy of my initial question), and it would
> > make it less insulting.
> >
> >
> > Alex
> >
> >
> >
> >   >
> >
> > Hi,
> >
> > Googling things like "gromacs DNA structure" is a good bet. There are no
> > fully standardised naming schemes or workflows, so you will likely not
> have
> > something do everything for you.
> >
> > Mark
> >
> > On 03/04/2015 7:03 am, "Alex" <nedomacho at gmail.com> wrote:
> >
> >
> > I'm fully aware that this is a forum for discussing Gromacs, but there's
> a
> > bit of a frustrating situation that involves using it.
> >
> > I need a linear ssDNA chain, sequence of my choosing, anything that will
> > work with, say, AMBER99SB-ILDN. Not trying to find any funny forcefields
> > for it, everything as is. You suggested AMBER in the past, so AMBER it
> is.
> >
> >
> > ChemOffice produced a PDB with incompatible atom types. make-na server (
> > http://structure.usc.edu/make-na/server.html) also produced something
> > pdb2gmx hates. Is there absolutely any way to get a PDB that will
> produce a
> > usable topology out of the box with an established potential implemented
> in
> > Gromacs? Anything that will not involve manual modification of PDBs or
> > writing text-processing scripts will make me very happy.
> >
> >
> > I will really appreciate any suggestions.
> >
> >
> > Thank you,
> >
> >
> > Alex
> >
> >
> >
> >
> > --
> >
> > 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.
> >
> >
> >
> >
> >
> > --
> >
> > Best regards,
> >
> >  Alex                            mailto:nedomacho at gmail.com
> > <nedomacho at gmail.com>
> >
> > --
> > 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.
> >
>
>
> ------------------------------
>
> Message: 5
> Date: Fri, 3 Apr 2015 17:53:03 +0200
> From: Mark Abraham <mark.j.abraham at gmail.com>
> To: Alex <nedomacho at gmail.com>,         Discussion list for GROMACS users
>         <gmx-users at gromacs.org>
> Subject: Re: [gmx-users] GMX-compatible DNA coordinates
> Message-ID:
>         <CAMNuMAT21AC1oJ6Un=
> 122-_kpx5-Ju6QGLrXKvQxAgyFNpBh6w at mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> Hi,
>
> I tried that search myself and found some things that looked potentially
> useful to you, so I suggested that search. Either you might find something
> useful there, or the dialogue could progress about what you need. Requiring
> perfect input for pdb2gmx is a fairly stringent expectation.
>
> Mark
> On 03/04/2015 3:40 pm, "Alex" <nedomacho at gmail.com> wrote:
>
> >  Mark,
> >
> >
> > Not to troll, but why did you assume that I didn't do my due diligence
> > before posting here?
> >
> > Because, you see, you could have left that second part of your reply
> > (which only confirms the legitimacy of my initial question), and it would
> > make it less insulting.
> >
> >
> > Alex
> >
> >
> >
> >   >
> >
> > Hi,
> >
> > Googling things like "gromacs DNA structure" is a good bet. There are no
> > fully standardised naming schemes or workflows, so you will likely not
> have
> > something do everything for you.
> >
> > Mark
> >
> > On 03/04/2015 7:03 am, "Alex" <nedomacho at gmail.com> wrote:
> >
> >
> > I'm fully aware that this is a forum for discussing Gromacs, but there's
> a
> > bit of a frustrating situation that involves using it.
> >
> > I need a linear ssDNA chain, sequence of my choosing, anything that will
> > work with, say, AMBER99SB-ILDN. Not trying to find any funny forcefields
> > for it, everything as is. You suggested AMBER in the past, so AMBER it
> is.
> >
> >
> > ChemOffice produced a PDB with incompatible atom types. make-na server (
> > http://structure.usc.edu/make-na/server.html) also produced something
> > pdb2gmx hates. Is there absolutely any way to get a PDB that will
> produce a
> > usable topology out of the box with an established potential implemented
> in
> > Gromacs? Anything that will not involve manual modification of PDBs or
> > writing text-processing scripts will make me very happy.
> >
> >
> > I will really appreciate any suggestions.
> >
> >
> > Thank you,
> >
> >
> > Alex
> >
> >
> >
> >
> > --
> >
> > 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.
> >
> >
> >
> >
> >
> > --
> >
> > Best regards,
> >
> >  Alex                            mailto:nedomacho at gmail.com
> > <nedomacho at gmail.com>
> >
> > --
> > 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.
> >
>
>
> ------------------------------
>
> --
> 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.
>
> End of gromacs.org_gmx-users Digest, Vol 132, Issue 13
> ******************************************************
>