Problem creating pNNMAKE.gnu

[Anonymous]

Hi,

I have installed ROSETTA3.1 on a AMD 64bit machine. However I am not able to “make” pNNMAKE.gnu which is required by make_fragments.pl program. I am getting when I type “make” in the rosetta_fragments/nnmake directory:

---

[anirbang@biogene nnmake]$ make

---

SYSTEM SETUP [make.system]
COMPILER=gnu @ biogene.npsf.cdac.ernet.in
F77=g77
FFLAGS=-finline-functions -funroll-loops -W -ffixed-line-length-132 -Wimplicit -O -ffast-math -malign-double
FOPTIMFLAGS=-O -ffast-math -malign-double
FDEBUGFLAGS=-g -Wall -Wimplicit -Wsurprising -Wformat -W
FPROFILEFLAGS=-pg
LINKFLAGS=

---

g77 -finline-functions -funroll-loops -W -ffixed-line-length-132 -Wimplicit -O -ffast-math -malign-double -c -o .gnu.make_ss_nn.o make_ss_nn.f
make_ss_nn.f:0: error: -malign-double makes no sense in the 64bit mode
make: *** [.gnu.make_ss_nn.o] Error 1

---

Please suggest a solution.

Regards,

—
Anirban Ghosh
Grade Based Engineer
Bioinformatics Team
Scientific & Engineering Computing Group
Centre for Development of Advanced Computing
Pune, India

[Anonymous]

I don’t know anything about the fragments machinery, but I will point out the Robetta server which is a web interface to the fragment generator: http://robetta.bakerlab.org/fragmentsubmit.jsp

[Anonymous]

I have the same problem,too.
I want to build my own fragments with different size,not only 3 aa or 9 aa,So the Robetta sever cann’t help,Could any one sovle the problem,please?
3Q!
jianhong zhou
China pharmeceutical University

> Hi,
>
> I have installed ROSETTA3.1 on a AMD 64bit machine. However I am not able to “make” pNNMAKE.gnu which is required by make_fragments.pl program. I am getting when I type “make” in the rosetta_fragments/nnmake directory:
>

---

> [anirbang@biogene nnmake]$ make
>

---

> SYSTEM SETUP [make.system]
> COMPILER=gnu @ biogene.npsf.cdac.ernet.in
> F77=g77
> FFLAGS=-finline-functions -funroll-loops -W -ffixed-line-length-132 -Wimplicit -O -ffast-math -malign-double
> FOPTIMFLAGS=-O -ffast-math -malign-double
> FDEBUGFLAGS=-g -Wall -Wimplicit -Wsurprising -Wformat -W
> FPROFILEFLAGS=-pg
> LINKFLAGS=
>

---

> g77 -finline-functions -funroll-loops -W -ffixed-line-length-132 -Wimplicit -O -ffast-math -malign-double -c -o .gnu.make_ss_nn.o make_ss_nn.f
> make_ss_nn.f:0: error: -malign-double makes no sense in the 64bit mode
> make: *** [.gnu.make_ss_nn.o] Error 1
>

---

>
> Please suggest a solution.
>
>
> Regards,
>
>
>
> —
> Anirban Ghosh
> Grade Based Engineer
> Bioinformatics Team
> Scientific & Engineering Computing Group
> Centre for Development of Advanced Computing
> Pune, India

[Anonymous]

hah,I have solved the problem.
open the make.system file at the nnmake dir,
delete the L67 like this: $FOPTIMFLAGS=-o -ffast-match -malign-double ,just add # at the front.
[HengZheng@localhost nnmake]$ $make
the compileing is ok!!
then type ./pNNMAKE.gnu at the terminal;
1./
2./
3./
4/net/shared/nnmake_database/
5./
6./
7./
8./
9./
10./
11./
12./
13/scratch/shared/nnmake_database/
14./
15./
16./
17./
NNMAKE requires three arguments
prefix code (char*2),
pdb name in lowercase (char*4)
chain name (char*1, ‘_’ for none)
e.g. ‘pNNMAKE ta 1ubq _ ‘

4 arguments required for forcing barcodes:
pNNMAKE code pdbname chain -barcode_file file
OR tries pdbnamechain.bar

4 arguments required for making loop libraries:
pNNMAKE code pdbname chain zone_file
OR
pNNMAKE code pdbname chain -zonelist filename

NOTE: zone files should be base name for zones,
template pdb, template ssa, and loop files

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