Well. At this point I'm going to declare your amber11 directory officially
borked (with what little-to-no authority a grad student has to make
official statements). My suggestion is to extract a fresh copy. The
spaces present in the Makefiles are ominous, since those _don't_ exist in
the distribution tarballs, and no patch converts them to spaces. Thus,
something must have happened. Even if you did get it to compile, I would
not be surprised to see a large number of the tests fail for whatever
reason.
This new error suggests a busted patch application -- specifically bugfix.3
for AmberTools 1.5 which adds the SCEE and SCNB scaling to the topology
file in tleap. Can you extract a fresh copy and reinstall?
All the best,
Jason
On Tue, Jan 24, 2012 at 3:08 PM, Ismail, Mohd F. <farid.ou.edu> wrote:
> I am using CentOS 6 (now CentOS 6.2 after all the updates), and I did a
> clean install of Amber11 and Ambertools 1.5 last week. Everything was
> smooth. Maybe the error is somewhere else?
>
> --Farid
> ________________________________________
> From: Irene Newhouse [einew.hotmail.com]
> Sent: Tuesday, January 24, 2012 2:01 PM
> To: amber.ambermd.org
> Subject: Re: [AMBER] AmberTools 1.5 & Centos6
>
> 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
>
> _______________________________________________
> 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
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Received on Tue Jan 24 2012 - 13:00:02 PST
