[gmx-users] Re: dPCA
Gia Maisuradze
gia at chem.unr.edu
Wed Oct 19 21:31:15 CEST 2005
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?
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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