Hi Dr. Cheatham:
Thank you for your response. I downloaded the new ptraj from the
website you gave me. I use this to overwrite the old one. But when I
compile the whole program, it stopped at carnal.
make[1]: Leaving directory
`/opt/programs/amber7-10TIMES-ERR/src/sander'
cd ptraj; make install
make[1]: Entering directory `/opt/programs/amber7-10TIMES-ERR/src/ptraj'
cd pdb; make
make[2]: Entering directory
`/opt/programs/amber7-10TIMES-ERR/src/ptraj/pdb'
make[2]: Nothing to be done for `all'.
make[2]: Leaving directory
`/opt/programs/amber7-10TIMES-ERR/src/ptraj/pdb'
cc -g -DDEBUG -g -DDEBUG main.o rdparm.o dispatch.o help.o utility.o
io.o trajectory.o torsion.o rms.o display.o interface.o energy.o
experimental.o ptraj.o actions.o analyze.o -o rdparm pdb/libpdb.a -lm
cd pdb; make
make[2]: Entering directory
`/opt/programs/amber7-10TIMES-ERR/src/ptraj/pdb'
make[2]: Nothing to be done for `all'.
make[2]: Leaving directory
`/opt/programs/amber7-10TIMES-ERR/src/ptraj/pdb'
cc -g -DDEBUG -g -DDEBUG main.o rdparm.o dispatch.o help.o utility.o
io.o trajectory.o torsion.o rms.o display.o interface.o energy.o
experimental.o ptraj.o actions.o analyze.o -o ptraj pdb/libpdb.a -lm
mkdir: cannot create directory `../../exe': File exists
make[1]: [install] Error 1 (ignored)
/bin/mv rdparm ptraj ../../exe
make[1]: Leaving directory `/opt/programs/amber7-10TIMES-ERR/src/ptraj'
cd carnal; make install
make[1]: Entering directory
`/opt/programs/amber7-10TIMES-ERR/src/carnal'
.../Compile LOADCC -o carnal main.o util.o rdprm.o static.o stream.o
group.o table.o pointax.o coord.o doit.o geom.o meas.o pdbgen.o modsel.o
hbond.o stats.o distrib.o rms.o matrix3.o pucker.o dme.o image.o
energy.o cutres.o -lm
g77 -O6 -o carnal main.o util.o rdprm.o static.o stream.o group.o
table.o pointax.o coord.o doit.o geom.o meas.o pdbgen.o modsel.o hbond.o
stats.o distrib.o rms.o matrix3.o pucker.o dme.o image.o energy.o
cutres.o -lm -lm
util.o(.text+0x1a48): In function `tokint':
: undefined reference to `__ctype_b'
util.o(.text+0x1ae8): In function `tokREAL':
: undefined reference to `__ctype_b'
collect2: ld returned 1 exit status
make[1]: *** [carnal] Error 1
make[1]: Leaving directory `/opt/programs/amber7-10TIMES-ERR/src/carnal'
make: *** [install] Error 2
But I didn't do anything to carnal. I just wonder whether I should
delete the old ptraj first then move the new one in. Because when I
check the files in /ptraj/pdb directory, I find out that the old ptraj
and the new one do not have the same amount of files there.
Best,
Lishan
On Wed, 2003-08-20 at 15:00, Thomas E. Cheatham, III wrote:
> > I use ptraj to superimpose one MD trajectory for a diatomic molecule.
> > I got this error message. It seems that it crashes when reading
> > ANGLES_WITHOUT_HYDROGEN. In my case there is no angle. So, could you
> > tell me how to fix this? Thanks.
>
> There are two issues; one you need to get the bug fix to allow proper
> reading of the new style prmtop (when no angles, etc are present). This
> is available at http://www.chpc.utah.edu/~cheatham/software.html. I will
> look into putting an appropriate bug fix on the AMBER WWW pages.
>
> Second, RMSd fitting currently requires four atoms for a fit so it will
> not allow RMS fitting a diatomic. The "principal" command may work, but I
> don't know for sure. To use this,
>
> principal :1 dorotation
>
> where your diatomic is residue 1 (:1).
>
> Good luck,
>
> \ Thomas E. Cheatham, III (Assistant Professor) College of Pharmacy
> | Departments of Medicinal Chemistry and of University of Utah
> | Pharmaceutics and Pharmaceutical Chemistry 30 South 2000 East, Room 201
> | & Center for High Performance Computing Salt Lake City, Utah 84112
> |
> | e-mail: tec3.utah.edu phone: (801) 587-9652 FAX: (801) 585-9119
> \ http://www.chpc.utah.edu/~cheatham Offices: BPRP295A / INSCC 418
>
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--
Lishan Yao <yaolisha.pilot.msu.edu>
MSU
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Received on Mon Aug 25 2003 - 14:53:00 PDT
