[gmx-users] g_covar to calculate correlation of motion
bipin singh
bipinelmat at gmail.com
Mon Feb 21 10:58:24 CET 2011
Thanks a lot Sir.
On Mon, Feb 21, 2011 at 15:26, Tsjerk Wassenaar <tsjerkw at gmail.com> wrote:
> Hi Bipin,
>
> The file residuetypes.dat is quite different from aminoacids.dat. You
> can paste the following into that file (first line is number of
> entries, followed by so many residue names):
>
> 49
> ABU
> ACE
> AIB
> ALA
> ARG
> ARGN
> ASN
> ASN1
> ASP
> ASP1
> ASPH
> CYS
> CYS1
> CYS2
> CYSH
> DALA
> GLN
> GLU
> GLUH
> GLY
> HIS
> HIS1
> HISA
> HISB
> HISH
> HYP
> ILE
> LEU
> LYS
> LYSH
> MELEU
> MET
> MEVAL
> NAC
> NH2
> PHE
> PHEH
> PHEU
> PHL
> PRO
> SER
> THR
> TRP
> TRPH
> TRPU
> TYR
> TYRH
> TYRU
> VAL
>
>
> Groetjes,
>
> Tsjerk
>
> On Mon, Feb 21, 2011 at 8:47 AM, bipin singh <bipinelmat at gmail.com> wrote:
> > Hi,
> > Thanks for your suggestion.
> > While running the g_covar it is showing the error that aminoacids.dat is
> not
> > found, so i have copied the residuetypes.dat(which i seems the new
> modified
> > name for aminoacids.dat in current GROMACS version), then it prompts to
> > choose the group for least square fit, which is not usual groups(i.e
> protein
> > or C alpha groups etc.).....please suggest where i have made mistake.
> >
> > Choose a group for the least squares fit
> > Opening library file aminoacids.dat
> > WARNING 2 [file aminoacids.dat, line 1]:
> > File aminoacids.dat is empty
> > Group 0 ( System) has 30585 elements
> > Group 1 ( GLU) has 47 elements
> > Group 2 ( HIS) has 86 elements
> > Group 3 ( ASN) has 224 elements
> > Group 4 ( PRO) has 56 elements
> > Group 5 ( VAL) has 272 elements
> > Group 6 ( MET) has 68 elements
> > Group 7 ( GLY) has 168 elements
> > Group 8 ( ILE) has 190 elements
> > Group 9 ( ALA) has 110 elements
> > Group 10 ( SER) has 143 elements
> > Group 11 ( PHE) has 80 elements
> > Group 12 ( LYS) has 242 elements
> > Group 13 ( TYR) has 189 elements
> > Group 14 ( LEU) has 304 elements
> > Group 15 ( GLN) has 102 elements
> > Group 16 ( TRP) has 48 elements
> > Group 17 ( ARG) has 120 elements
> > Group 18 ( ASP) has 108 elements
> > Group 19 ( THR) has 141 elements
> > Group 20 ( SOL) has 27882 elements
> > Group 21 ( CL) has 5 elements
> >
> >
> > On Mon, Feb 21, 2011 at 12:44, Tsjerk Wassenaar <tsjerkw at gmail.com>
> wrote:
> >>
> >> Hi Bipin,
> >>
> >> Try using a .gro or .pdb file as reference structure (-s). Only .tpr
> files
> >> are version specific.
> >>
> >> Cheers,
> >>
> >> Tsjerk
> >>
> >> On Feb 21, 2011 8:05 AM, "bipin singh" <bipinelmat at gmail.com> wrote:
> >>
> >> Dear GMX users,
> >>
> >> I want to calculate the correlated motion between atoms during the md
> >> simulation
> >>
> >> for that purpose I am using g_covar(the one which is available under
> >> http://www.gromacs.org/Downloads/User_contributions/Other_software)
> >>
> >>
> >>
> >> but it is not compatible with the GROMACS-4.5.3, so please suggest me
> the
> >> alternative way or does anyone have the modified g_covar for
> >> GROMKACS-4.5.3.
> >>
> >> --
> >> ---------------------------------
> >> Thanks and regards
> >> Bipin Singh
> >>
> >>
> >> --
> >> gmx-users mailing list gmx-users at gromacs.org
> >> http://lists.gromacs.org/mailman/listinfo/gmx-users
> >> Please search the archive at
> >> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> >> Please don't post (un)subscribe requests to the list. Use the
> >> www interface or send it to gmx-users-request at gromacs.org.
> >> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >>
> >> --
> >> gmx-users mailing list gmx-users at gromacs.org
> >> http://lists.gromacs.org/mailman/listinfo/gmx-users
> >> Please search the archive at
> >> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> >> Please don't post (un)subscribe requests to the list. Use the
> >> www interface or send it to gmx-users-request at gromacs.org.
> >> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> >
> >
> > --
> > ---------------------------------
> > Thanks and regards
> > Bipin Singh
> >
> >
> > --
> > gmx-users mailing list gmx-users at gromacs.org
> > http://lists.gromacs.org/mailman/listinfo/gmx-users
> > Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> > Please don't post (un)subscribe requests to the list. Use the
> > www interface or send it to gmx-users-request at gromacs.org.
> > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
>
>
>
> --
> Tsjerk A. Wassenaar, Ph.D.
>
> post-doctoral researcher
> Molecular Dynamics Group
> * Groningen Institute for Biomolecular Research and Biotechnology
> * Zernike Institute for Advanced Materials
> University of Groningen
> The Netherlands
> --
> gmx-users mailing list gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
--
*
---------------------------------
Thanks and regards
Bipin Singh
*
*
*
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20110221/f8d1f10c/attachment.html>
More information about the gromacs.org_gmx-users
mailing list