Now that you mention bugfixes - when I went to get the latest bugfix.all, instead of downloading as a file, it opened in a text window & I had to copy & paste it to a file. I wonder if that didn't cause problems? I won't know for a while, because I'm downloading another package & it's going slowly -- internet speeds are horrendous here-- so it will be a while before I've got fresh copies of Tools1.5 & the bugfixes. Thanks! Irene> Date: Tue, 24 Jan 2012 15:32:05 -0500
> From: jason.swails.gmail.com
> To: amber.ambermd.org
> Subject: Re: [AMBER] AmberTools 1.5 & Centos6
>
> 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
> _______________________________________________
> 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
Received on Tue Jan 24 2012 - 13:30:03 PST
