I have now moved onto a bigger & better error:
parmSet.c: In function ‘iParmSetAddProperTerm’:
parmSet.c:1610: error: ‘TORSIONPARMt’ has no member named ‘dScee’
parmSet.c:1610: error: ‘dScee’ undeclared (first use in this function)
parmSet.c:1610: error: (Each undeclared identifier is reported only once
parmSet.c:1610: error: for each function it appears in.)
parmSet.c:1611: error: ‘TORSIONPARMt’ has no member named ‘dScnb’
parmSet.c:1611: error: ‘dScnb’ undeclared (first use in this function)
parmSet.c: In function ‘ParmSetTORSIONTerm’:
parmSet.c:2042: error: ‘dPScee’ undeclared (first use in this function)
parmSet.c:2042: error: ‘TORSIONPARMt’ has no member named ‘dScee’
parmSet.c:2043: error: ‘dPScnb’ undeclared (first use in this function)
parmSet.c:2043: error: ‘TORSIONPARMt’ has no member named ‘dScnb’
parmSet.c: In function ‘bParmSetTORSIONAddProperTerm’:
parmSet.c:2075: error: ‘TORSIONPARMt’ has no member named ‘dScee’
parmSet.c:2075: error: ‘dScee’ undeclared (first use in this function)
parmSet.c:2076: error: ‘TORSIONPARMt’ has no member named ‘dScnb’
parmSet.c:2076: error: ‘dScnb’ undeclared (first use in this function)
parmSet.c: In function ‘bParmSetTORSIONAddImproperTerm’:
parmSet.c:2115: error: ‘TORSIONPARMt’ has no member named ‘dScee’
parmSet.c:2115: error: ‘dScee’ undeclared (first use in this function)
parmSet.c:2116: error: ‘TORSIONPARMt’ has no member named ‘dScnb’
parmSet.c:2116: error: ‘dScnb’ undeclared (first use in this function)
parmSet.c: In function ‘ParmSetTorsion’:
parmSet.c:2556: error: ‘dPScee’ undeclared (first use in this function)
parmSet.c:2556: error: ‘TORSIONPARMt’ has no member named ‘dScee’
parmSet.c:2557: error: ‘dPScnb’ undeclared (first use in this function)
parmSet.c:2557: error: ‘TORSIONPARMt’ has no member named ‘dScnb’
parmSet.c: In function ‘ParmSetImproper’:
parmSet.c:2600: error: ‘dPScee’ undeclared (first use in this function)
parmSet.c:2600: error: ‘TORSIONPARMt’ has no member named ‘dScee’
parmSet.c:2601: error: ‘dPScnb’ undeclared (first use in this function)
parmSet.c:2601: error: ‘TORSIONPARMt’ has no member named ‘dScnb’
parmSet.c: In function ‘ParmSetUpdateTorsion’:
parmSet.c:2772: error: ‘dPScee’ undeclared (first use in this function)
parmSet.c:2772: error: ‘TORSIONPARMt’ has no member named ‘dScee’
parmSet.c:2773: error: ‘dPScnb’ undeclared (first use in this function)
parmSet.c:2773: error: ‘TORSIONPARMt’ has no member named ‘dScnb’
parmSet.c: In function ‘ParmSetUpdateImproper’:
parmSet.c:2810: error: ‘dPScee’ undeclared (first use in this function)
parmSet.c:2810: error: ‘TORSIONPARMt’ has no member named ‘dScee’
parmSet.c:2811: error: ‘dPScnb’ undeclared (first use in this function)
parmSet.c:2811: error: ‘TORSIONPARMt’ has no member named ‘dScnb’
make[2]: *** [parmSet.o] Error 1
make[2]: Leaving directory `/opt/amber11/AmberTools/src/leap/src/leap'
make[1]: *** [install] Error 2
make[1]: Leaving directory `/opt/amber11/AmberTools/src/leap'
make: *** [serial] Error 2
What I find so particularly puzzling is that the process was smooth with Centos5.x, but now with Centos6, I'm running into all these bizarre situations! I've attached parmset.c, since that seems to be where the issue is. I note that there's also a parmset.c.orig in the distribution, & that there was a Makefile.orig in the pbsa directory. Possibly not a coincidence? Thanks again for your help.
Irene
> Date: Tue, 24 Jan 2012 13:16:44 -0500
> From: jason.swails.gmail.com
> To: amber.ambermd.org
> Subject: Re: [AMBER] AmberTools 1.5 & Centos6
>
> I meant the pbsa/Makefile, sorry for any confusion.
>
> On Tue, Jan 24, 2012 at 12:22 PM, Irene Newhouse <einew.hotmail.com> wrote:
>
> >
> > I've attached the Makefile, which I haven't changed. Line 208 seems to be
> > tabbed just like the others. I looked at the error messages & the cd to
> > $AMBERHOME/AmberTools/src/pbsa is line 197. It is also tabbed, not spaced,
> > as nearly as I can tell - that is, all the lines in that neighborhood react
> > to the cursor the same: I can use the arrow key to place the cursor in the
> > space immediately to the left of the first printing character & nowhere
> > further to the left.
> >
> > Thanks!
> > Irene
> >
> > > Date: Mon, 23 Jan 2012 16:35:43 -0500
> > > From: jason.swails.gmail.com
> > > To: amber.ambermd.org
> > > Subject: Re: [AMBER] AmberTools 1.5 & Centos6
> > >
> > > Can you post your $AMBERHOME/AmberTools/src/pbsa/Makefile here? A quick
> > > google suggests that this error is caused because line 208 of that
> > Makefile
> > > is using spaces instead of tabs to indent a line. Can you verify that
> > this
> > > is true? If it is true, can you replace those spaces with a tab?
> > >
> > > On Mon, Jan 23, 2012 at 2:49 PM, Irene Newhouse <einew.hotmail.com>
> > wrote:
> > >
> > > >
> > > > I had had an AmberTools 1.5 installation on my linux box under
> > Centos5.x.
> > > > I recently upgraded to Centos6 & tried to reinstall. I have gcc 4.4.6
> > and
> > > > flex 2.5.35-8. Yes, I downloaded the latest version of the bugfixes,
> > and
> > > > patched successfully. The make goes a long way, and then crashes:
> > > >
> > > > make[1]: Leaving directory `/opt/amber11/AmberTools/src/chamber'
> > > > (cd pbsa && make install )
> > > > make[1]: Entering directory `/opt/amber11/AmberTools/src/pbsa'
> > > > Makefile:208: *** missing separator. Stop.
> > > > make[1]: Leaving directory `/opt/amber11/AmberTools/src/pbsa'
> > > > make: *** [serial] Error 2
> > > >
> > > > Does anyone have any advice for me?
> > > >
> > > > Thanks!
> > > > Irene Newhouse
> > > >
> > > >
> > > >
> > > >
> > > > _______________________________________________
> > > > AMBER mailing list
> > > > AMBER.ambermd.org
> > > > http://lists.ambermd.org/mailman/listinfo/amber
> > > >
> > >
> > >
> > >
> > > --
> > > Jason M. Swails
> > > Quantum Theory Project,
> > > University of Florida
> > > Ph.D. Candidate
> > > 352-392-4032
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> >
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> >
>
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
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Received on Tue Jan 24 2012 - 12:30:02 PST
