[gmx-users] g_covar to calculate correlation of motion

[bipin singh]

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
*
*
*
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20110221/03275105/attachment.html>