[gmx-users] using the correct .rtp files
David L. Bostick
dbostick at physics.unc.edu
Thu Jun 19 18:33:00 CEST 2003
One more suggestion,..
IN a worst case scenario, you can always set the includes in the mdp file
to the explicit path ...
i.e. instead of
include = -I$GMXDATA/top
do
include = -I/usr/local/my/crazy/long/path/top
to make grompp search only that directory and your current working
directory. At least then you wouldn't have to keep copies of your topology
in your current working directory.. If that doesn't work, I'd say you have
a much deeper problem than path variables..
Good luck,
David
-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
David Bostick Office: 262 Venable Hall
Dept. of Physics and Astronomy Phone: (919)962-0165
Program in Molecular and Cellular Biophysics
UNC-Chapel Hill
CB #3255 Phillips Hall dbostick at physics.unc.edu
Chapel Hill, NC 27599 http://www.unc.edu/~dbostick
=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-
On Thu, 19 Jun 2003, Paul Barrett wrote:
> No problem: thanks for replying at all.
>
> I think you must be right that something is set wrong somewhere else but
> I havent found it yet.
>
> As to your (sensible) suggestions:
> 1)where $GMXDATA points seems to be irrelavent somehow! if I set it to
> /usr or /etc or indeed anywhere, pdb2gmx still goes to the new /top
> directory.
> 2) Im not opening up a new shell between setting GMXDATA and running
> pdb2gmx
> 3) it cant be the .mdp file because Im not using one with pdb2gmx
>
> thanks for the time you have given anyhow
>
>
> Paul
>
>
> >
> >oops... responding too quickly..
> >
> >sounds like you have something set somewhere else. All I can suggest then
> >is to check to make sure $GMXDATA points to the right place before
> >grommpping.
> >
> >echo $GMXDATA
> >
> >if you source the GMXRC file in your .cshrc or something, you might get
> >GMXDATA pointing to the new version upon opening a new shell. Also check
> >your include line in your input mdp file...
> >
> >i.e.
> >
> >include = -I$GMXDATA/top -I/$GMXDATA/my_ffields
> >
> >etc...
> >
> >Hope it helps.. sorry for not reading carefully
> >David
> >
> >-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
> >David Bostick Office: 262 Venable Hall
> >Dept. of Physics and Astronomy Phone: (919)962-0165
> >Program in Molecular and Cellular Biophysics
> >UNC-Chapel Hill
> >CB #3255 Phillips Hall dbostick at physics.unc.edu
> >Chapel Hill, NC 27599 http://www.unc.edu/~dbostick
> >=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-
> >
> >On Thu, 19 Jun 2003, Paul Barrett wrote:
> >
> >> Thanks David.
> >>
> >> What do you make of the experience I described in the background that
> >> shows the GMXDATA variable does not seem to work.
> >>
> >> Paul
> >>
> >> >
> >> >Hi,
> >> >
> >> >setenv GMXDATA directory_name
> >> >
> >> >where directory_name = old /share directory from previous gmx installation.
> >> >
> >> >David
> >> >
> >> >-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
> >> >David Bostick Office: 262 Venable Hall
> >> >Dept. of Physics and Astronomy Phone: (919)962-0165
> >> >Program in Molecular and Cellular Biophysics
> >> >UNC-Chapel Hill
> >> >CB #3255 Phillips Hall dbostick at physics.unc.edu
> >> >Chapel Hill, NC 27599 http://www.unc.edu/~dbostick
> >> >=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-
> >> >
> >> >On Thu, 19 Jun 2003, Paul Barrett wrote:
> >> >
> >> >> Hi
> >> >>
> >> >> Summary:
> >> >> --------
> >> >>
> >> >> What is the (environment?) variable I need to change to get a new
> >> >> installation of GROMACS to use the /top files from a previous
> >> >> installation. (I may not edit the /top files from the new
> >> >> installation.)
> >> >>
> >> >> i.e. How do I redirect GROMACS to look in my old /top directory for .rtp
> >> >> files
> >> >>
> >> >> Background
> >> >> ----------
> >> >>
> >> >> I have been using GROMACS for a while successfully.
> >> >>
> >> >> I now want to run a version of GROMACS owned by another group. By
> >> >> sourcing the appropriate GMXRC my machine correctly runs using the new
> >> >> copy of the program
> >> >>
> >> >> However I want to continue to use the old files from /top , for example
> >> >> ffGMX43a1.rtp which I have edited.
> >> >>
> >> >> I thought it would be a case of setenv $GMXDATA to the directory that
> >> >> contains /top, however this does not work: e.g. pdb2gmx continues to
> >> >> refer to the /top files in the new installation.
> >> >>
> >> >> Indeed if I change $GMXDATA to somewhere altogether wrong pdb2gmx
> >> >> continues to use the /top from the new installation.
> >> >>
> >> >> I have got it to work by copying the .rtp (etc) files in to the
> >> >> directory where I am running pdb2gmx but this is not an acceptable long
> >> >> term solution for me.
> >> >>
> >> >> How do I redirect GROMACS to look in my old /top directory?
> >> >>
> >> >> many thanks
> >> >>
> >> >> Paul Barrett
> >> >> University of Oxford
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