[gmx-users] Re: dPCA
David
spoel at xray.bmc.uu.se
Wed Oct 19 22:33:44 CEST 2005
On Wed, 2005-10-19 at 12:31 -0700, Gia Maisuradze wrote:
> Dear David,
>
> Thanks for you reply. I am trying to get phi and psi dihedrals by using
> g_chi, but so far I got C(t) for phi and psi of each residue, also I got phi
> and psi as a function of residue number (order.xvg). I think they are
> averaged over the time. Is this what I need for index file? Is there any
> other option to obtain psi and phi? To make the index file I need more
> information apart from those I have got. Do you know what commands could I
> use to obtain a complete information for index file?
you just need to go through a pdb file and write down the atom numbers
for each phi and psi dihedral
[ dihs ]
1 3 5 7
3 5 7 9
etc.
>
> Thanks in advance,
>
> Gia
>
> ----- Original Message -----
> From: "David van der Spoel" <spoel at xray.bmc.uu.se>
> To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
> Sent: Wednesday, October 19, 2005 12:01 AM
> Subject: Re: [gmx-users] Re: dPCA
>
>
> > On Tue, 2005-10-18 at 14:25 -0700, Gia Maisuradze wrote:
> >> Dear David,
> >>
> >> Thanks for your reply. I have seen -or option in Gromacs 3.3 RC2 version
> >> and
> >> made a trajectory file from g_angle. Then I have generated new topology
> >> file
> >> (tpr) for dihedral angles by using tpbconv. After that I used trr
> >> (obtained
> >> from g_angle) and tpr (obtained from tpbconv) and angle.ndx (obtained
> >> from
> >> mk_angndx) in g_covar to get eigenvactors and eigenvalues, and I got
> >> Segmentation fault. When I was creating all these files I was asked which
> >> group of dihedrals I want to include, I have picked one of them for all
> >> files (I don't know the comand which can include all groups).
> > You probably have to make your own index file for g_angle containing all
> > phi and psi dihedrals in the order you wish. Then you have to create a
> > tpr file containing (2*N)/3 atoms, where N is the number of dihedrals.
> > Since there are two values stored per dihedral, there will be 2*N
> > entries, but since atoms always have three coordinates the number is
> > rounded up. So for 8 dihedrals, you have 16 values which is rounded up
> > to 18 to make a multiple of three. You then need a tpr file with 6
> > atoms.
> >
> >>
> >> I don't know why I got segmentation fault, any idea? Could it be related
> >> to
> >> index file?
> >>
> >> Thanks in advance,
> >>
> >> Gia
> >>
> >> ----- Original Message -----
> >> From: "David van der Spoel" <spoel at xray.bmc.uu.se>
> >> To: <gmx-users at gromacs.org>
> >> Sent: Monday, October 17, 2005 10:29 PM
> >> Subject: [gmx-users] Re: dPCA
> >>
> >>
> >> > On Mon, 2005-10-17 at 17:51 -0700, Gia Maisuradze wrote:
> >> >> David,
> >> >>
> >> >> I have tried to do dPCA on Gromacs 3.3 RC2. First, I have generated
> >> >> angle.ndx by using mk_angndx where in option -type I wrote dihedral,
> >> >> ryckaert-bellemans or phi-psi option does not work. So my angle.ndx
> >> >> looks
> >> >> like:
> >> >> [ Phi=180.0_2_7.11 ]
> >> >> 1 2 4 5
> >> >> [ Phi=180.0_2_33.5 ]
> >> >> 2 4 6 8 8 10 12 14 14 16 18
> >> >> 20
> >> >>
> >> >> [ Phi=180.0_6_1 ]
> >> >> 4 6 7 9 10 12 14 16 16 18 20
> >> >> 22
> >> >>
> >> >> [ Phi=0.0_2_2.09 ]
> >> >> 5 4 6 8
> >> >> [ Phi=0.0_0_0 ]
> >> >> 7 6 8 9 19 20 22 23 20 22 25
> >> >> 24
> >> >> 20 22 25 26
> >> >> [ Phi=0.0_6_1 ]
> >> >> 6 8 10 12 12 14 16 18
> >> >>
> >> >> then I used angle.ndx along with trajectory and tpr files to produce
> >> >> trajectory file for dPCA. In g_angle I wrote for -type option
> >> >> dihedral.
> >> >> Also
> >> >> it asks the group to choose, each group has a different number of
> >> >> elements.
> >> >> Which one to pick? I found that -oc calculates dihedral
> >> >> autocorrelation
> >> >> function. My concern is I could not produce cos(phi) sin(phi) cos(psi)
> >> >> sin(psi), as we discussed in our one of the previous emails. Also, the
> >> >> dihedral autocorrelation function that I got from -oc option is in xvg
> >> >> format, for g_covar I need either xtc or trr format.
> >> >>
> >> >> Are steps described above correct to perform dPCA? Does Gromacs 3.3
> >> >> RC2
> >> >> support dPCA?
> >> > Use the -h option then you will see that you need -or
> >> > The index file you may need to make yourself.
> >> >
> >> > Please put further questions on the mailing list.
> >> >>
> >> >> Thanks in advance,
> >> >>
> >> >> Gia
> >> >>
> >> >> ----- Original Message -----
> >> >> From: "David" <spoel at xray.bmc.uu.se>
> >> >> To: "Gia Maisuradze" <gia at chem.unr.edu>
> >> >> Cc: <gmx-users at gromacs.org>
> >> >> Sent: Thursday, October 13, 2005 1:03 PM
> >> >> Subject: Re: dPCA
> >> >>
> >> >>
> >> >> > On Thu, 2005-10-13 at 11:48 -0700, Gia Maisuradze wrote:
> >> >> >> Dear David,
> >> >> >>
> >> >> >> I have checked the changes in new Gromacs 3.3. It says that
> >> >> >> dihedral
> >> >> >> PCA is supported in g_angle (you are the author). Does it mean that
> >> >> >> we
> >> >> >> can do dihedral principal component analysis for proteins? Is it
> >> >> >> the
> >> >> >> same type of analysis that has been done by Gerhard Stock' group
> >> >> >> (PROTEINS, 58, 45, 2005)? If yes, I don't clearly understand how I
> >> >> >> can
> >> >> >> do that. Normal PCA (in cartesian coordinates) can be done by using
> >> >> >> g_covar, where we build the covariance matrix and diagonalize it,
> >> >> >> and
> >> >> >> get eigenvectors and eigenvalues. Then analyze them.
> >> >> >>
> >> >> >> Could you, please, explain how I can do dPCA on Gromacs, if it is
> >> >> >> possible.
> >> >> > Yes, you use g_angle -oc to produce a new trajectory file
> >> >> > containing:
> >> >> > cos(phi) sin(phi) cos(psi) sin(psi) etc.
> >> >> > This you run through g_covar.
> >> >> >
> >> >> > According to some people this information is not really useful for
> >> >> > protein analysis, as it can show many false minima and it is hard to
> >> >> > go
> >> >> > back to real space. Barriers you see may be trivial due to
> >> >> > overlapping
> >> >> > atoms.
> >> >> >
> >> >> >
> >> >> >>
> >> >> >> The same question I have asked Erik Lindahl, but he did not know
> >> >> >> about
> >> >> >> dPCA in new Gromacs version.
> >> >> >>
> >> >> >> Thanks,
> >> >> >>
> >> >> >> Gia
> >> >> > --
> >> >> > 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
> >> >> > spoel at xray.bmc.uu.se spoel at gromacs.org
> >> >> > http://xray.bmc.uu.se/~spoel
> >> >> > ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> >> >> >
> >> >> >
> >> >
> >> > _______________________________________________
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--
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
spoel at xray.bmc.uu.se spoel at gromacs.org http://xray.bmc.uu.se/~spoel
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